Topic 7.1 Replication and DNA Structure

Report
7.1 DNA Structure &
Replication
Essential Idea: The structure of
DNA is ideally suited to its
function.
DNA is a double helix, consisting of two
anti-parallel chains of polynucleotides
that are held together by hydrogen
bonds between complementary bases
on the different strands. This structure
allows the double helix to be replicated,
with one ‘old’ strand combining
together with a new strand in semiconservative replication. And DNA is
transcribed into mRNA, which is then
translated into a polypeptide.
By Darren Aherne
DNA’s function is to transmit genetic
information from one generation to
the next. It is a stable macromolecule
that can be replicated with a high
degree of fidelity in the enzyme
assisted process of replication. These
copies are passed on from one
generation of cells to the next.
Understandings, Applications and Skills
Understandings, Applications and Skills
7.1 S1 Analysis of results of the Hershey and Chase experiment
providing evidence that DNA is the genetic material.
• Until the Hershey Chase experiment, it seemed that
protein was the genetic material because it had great
variety in structures
• Hershey & Chase took advantage of the fact that
DNA contains phosphorus, but not sulfur, & protein
contains sulfur, but not phosphorus. Viruses have
protein coats surrounding DNA.
• They grew viruses in two environments- type 1 with
radioactive phosphorus, and type 2 with radioactive
sulfur.
http://highered.mheducation.com/olc/dl/1
20076/bio21.swf
7.1.A1 Rosalind Franklin’s and Maurice Wilkins’
investigation of DNA structure by X-ray diffraction.
• When X-rays pass through a substance, they diffract.
• Crystals have a regularly repeating pattern, causing
X-rays to diffract in a regular pattern.
• These patterns allow for measurements &
calculations to be made about the structure of
molecules.
• X pattern: DNA is a helix
• Angle of X: Calculate the steepness of the
helix
• Distance between horizontal bars: Distance
between bases is 3.4nm.
• Distance between center of X and top of
image: .34nm vertically between the
repeating units (bases) in the molecule- so
10 bases per turn of the helix.
http://www.dnalc.org/view/15874Franklin-s-X-ray.html
7.1.Nature of Science: Making careful observations—Rosalind Franklin’s X-ray
diffraction provided crucial evidence that DNA is a double helix.
• Rosalind Franklin worked at King’s College in London as a
technician doing X-ray crystallography.
• She improved the resolution of the cameras used in order
to obtain the most detailed images yet of X-ray diffraction
of DNA.
• These detailed images allowed her to make very exact
measurements related to the structure of DNA.
• Her work was shared with James Watson without her
permission.
• Watson and Crick used her measurements to show that
the phosphate groups were on the outside of the DNA
double helix, and that the nitrogenous bases were more
hydrophobic and thus on the inside.
• Watson & Crick published the structure of DNA first,
without crediting Franklin. They were awarded the Nobel
prize. Franklin died of ovarian cancer she developed as a
result of her work.
Rosalind Franklin
http://en.wikipedia.org/wiki/Rosa
lind_Franklin
7.1.U2 DNA structure suggested a
mechanism for DNA replication.
Antiparallel Strands
• The two strands have their 5’ and 3’
terminals at opposite ends
3’ – 5’ Linkages
• 5’ end of a DNA strand- the deoxyribose
is linked to a phosphate
• 3’ end of a DNA strand- a hydroxyl (-OH)
is attached to the 3’ carbon in a
deoxyribose
• Nucleotides in a strand are linked by
covalent phosphodiester bonds, linking
the 3’ of one nucleotide to the
phosphate attached to the 5’ on the
adjacent nucleotide
https://sites.google.com/a/canacad.ac.jp/sl-hl-1-biology-4ferguson/04-dna/7-1-dna-structure-and-replication
7.1.U2 DNA structure suggested a
mechanism for DNA replication.
Hydrogen bonding
• Purines (2 ring bases-Adenine & Guanine)
form hydrogen bonds with pyrimidines (1
ring bases- cytosine and thymine).
• Replication is semi-conservative- one
“new” strand joins with one “old” strand.
• Complementary base pairing allows for
replication to occur by new bases forming
hydrogen bonds with old bases.
http://highered.mheducation.com/sites/0072943696/student_view0/chapter3/
animation__dna_replication__quiz_1_.html
7.1.U1 Nucleosomes help
to supercoil the DNA.
Nucleosomes
• DNA in eukaryotes is associated with proteins
called histones.
• The octomer & DNA combination is attached
to an H1 histone, forming a nucleosome.
• The nucleosome serves to protect the DNA
from damage and to allow long lengths of DNA
to be supercoiled
Supercoiling
• Supercoiling allows the chromosomes to be
mobile in mitosis & meiosis.
• Supercoiled DNA cannot be transcribed for
protein synthesis.
DNA is wrapped twice around
each nucleosome.
http://www.ib.bioninja.com.au/higherlevel/topic-7-nucleic-acids-and/71-dnastructure.html#previous-photo
7.1.S2 Utilization of molecular visualization software to analyse the
association between protein and DNA within a nucleosome.
Visit:
http://www.rcsb.org/pdb/101/motm.do?momID=7
and
http://www.rcsb.org/pdb/explore/jmol.do?structureI
d=1AOI&bionumber=1
Explore:
• Find the two copies of each histone protein by
locating their “tails”.
• Visualize the positively charged amino acids on the
nucleosome core. How do they play a role in the
association of the protein core with the negatively
charged DNA?
7.1.U3 DNA polymerases can only add
nucleotides to the 3’ end of a primer.
• DNA Polymerases are enzymes that add new
nucleotides to a growing strand of DNA in the
process of replication.
• DNA polymerase III is responsible for forming
covalent bonds between the nucleotides as
they are added to polynucleotide.
Replication happens in a 5’  3’ direction.
http://www.ib.bioninja.com.au/higherlevel/topic-7-nucleic-acids-and/72-dnareplication.html#previous-photo
i-biology.net
i-biology.net
i-biology.net
http://highered.mheducation.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/d
l/free/0072437316/120076/bio23.swf::How%20Nucleotides%20are%20Added%20in%2
0DNA%20Replication
i-biology.net
7.1.U4 DNA replication is continuous on the leading strand and
discontinuous on the lagging strand.
7.1.U5 DNA replication is carried out by a complex system of enzymes.
i-biology.net
i-biology.net
i-biology.net
i-biology.net
i-biology.net
http://highered.mheducation.com/olcweb/cgi/pl
uginpop.cgi?it=swf::535::535::/sites/dl/free/0072
437316/120076/micro04.swf::DNA%20Replicatio
n%20Fork
i-biology.net
Watch this animation about the function of DNA Gyrase:
http://highered.mheducation.com/sites/007299524
6/student_view0/chapter20/action_of_dna_gyrase.
html
The Enzymes & Molecules of DNA Replication:
DNA Gyrase
(topoisomerase)
Affects the degree of supercoiling of the bacterial
chromosome
Helicase:
Unwinds DNA & breaks H-bonds between base pairs
DNA Polymerase III
Attaches nucleotides in a 5’  3’ direction
RNA Primase
Leaves RNA primers on the lag strand
DNA Polymerase I
Removes RNA primers
DNA Ligase
Attaches Okazaki fragments together by forming covalent
bonds between nucleotides
Single Stranded
Binding Proteins
Bonds with single stranded DNA that has been opened by
helicase and prevents it from reforming a double helix
i-biology.net
7.1.U6 Some regions of DNA do not code for
proteins but have other important functions.
http://www.dbriers.com/tutorials/wpcontent/uploads/2013/12/Central_Dogma-GODSwikimedia.jpg
Genes are coding regions of DNA—
they code for a polypeptide.
• In humans, only about 1%-2% of
DNA codes for a polypeptide.
These coding regions are called
exons.
• The remainder of the DNA is noncoding.
• The non-coding regions are
typically made up of repetitive
sequences of DNA.
From Biology Course Companion, Allott, A, Oxford University
Press, 2014
Some Functions of Non-Coding Regions of DNA
Production of RNA
Some regions on DNA function to produce tRNA and rRNA
Gene expression
Non-coding regions can have an role in regulating the
expression of genes by promoting or inhibiting.
Telomeres
Telomeres are located on the ends of eukaryote
chromosomes, they have a protective function because
DNA cannot be replicated all the way to the ends, so
telomeres prevent loss of important genes.
• Non-coding regions within
genes are called introns.
http://www.webbooks.com/eLibrary/ON/B0/B10/05
MB10.html
7.1.A2 Use of nucleotides containing dideoxyribonucleic acid to stop
DNA replication in preparation of samples for base sequencing.
Determining the Base Sequence of a
DNA Sample
• Uses florescence
• Many copies of sample DNA &
materials needed to replicate it placed
in test tubes
• Samples include a few
dideoxyribonucleic acid nucleotides
with different florescence.
http://www.yourgenome.org/teacher
s/sequencing.shtml
• Dideoxyribonucleic acid nucleotides
stop replication when incorporated to
DNA.
• Gel Electrophoresis is used to separate
DNA by fragment size.
• Images of florescent fragments allow
for sequencing based on size.
7.1.A3 Tandem repeats are used in DNA profiling.
Variable Number Tandem Repeats
Locus: the location of a gene
(VNTR): are chromosomal regions
on a chromosome (plural: loci)
in which a short DNA sequence
(such as GC or AGCT) is repeated a
variable number of times end-toend at a single location (tandem
repeat).
Schematic of a VNTR in 4 alleles. Each rectangle
represents a repeated series of bases in DNA.
http://en.wikipedia.org/wiki/Variable_number_t
andem_repeat
Watch this video about some applications of VNTRspaternity testing and forensics
https://www.youtube.com/watch?v=DbR9xMXuK
7c
Where does the DNA for analyzing heredity come from?
Paternal heredity: Y-chromosome
Maternal heredity: Mitochondrial DNA
In this example, Locus A is a
tandem repeat of the motif GC:
there are four alleles, with two,
three, four, or five repeats
(A2, A3, A4, and A5,
respectively). Locus B is a
tandem repeat of the
motif AGCT: there are only two
alleles, with two or three
repeats (B2 and B3,
respectively).
The example shows a DNA fingerprint that includes both loci simultaneously. Individual
#1 is heterozygous at Locus A (A2 / A5) and homozygous at Locus 2 (B2 / B2: note that this
genotype gives a single-banded phenotype in the fingerprint). Individual #2 is
heterozygous at both loci: (A4 / A3 and B3 / B2) respectively). The two individuals are
distinguishable at either locus. Typical fingerprints include a dozen or more VNTR loci.`
From:
http://www.mun.ca/biology/scarr/V
Thanks to these fine folks,
and any others that I may
have forgotten!

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