DNA and Replication
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DNA and Replication
You pose an interesting question – There are different types of Human
DNA – which there are various classifications, Chromosomal DNA and
Mitochondrial DNA. There is also the DNA present from normal flora
microorganisms such as bacteria, viruses, mites, etc. Some of this
microorganism DNA may be significant, such as E. coli DNA in the gut
or Staphylococcus DNA on the skin. You even have DNA present from
viruses of bacteria such as phage DNA. Some human viruses may be
present in blood cells such as EBV, CMV in nerve cells like herpes
simplex 1, in skin cell like HPV (human papilloma virus) or integrated
into the Human Chromosomal DNA such as various retroviruses, like
human foamy virus, HTLV or HIV
Within Chromosomal DNA there is DNA that codes for genes- exons (mRNA
coding) and non coding regions called introns. There are regions of
DNA within the introns that are called endogenous retroviruses – these
regions have great similarity to retroviruses and may have disease
An Okazaki fragment is a relatively short fragment of DNA that is
created by primase and Pol III along the lagging strand (see DNA
replication). They are later removed by RNAse H, and the last
ribonucleotide is removed by and synthesized by Pol I. The nick, or a
broken phosphodiester bond remaining between the fragments is linked
together by DNA ligase
The replication fork is a structure which forms when DNA is ready to
replicate itself. It is created by topoisomerase, which breaks the
hydrogen bonds holding the two DNA strands together. The resulting
structure has two branching "prongs", each one made up of a single
strand of DNA. DNA polymerase then goes to work on creating new
partners for the two strands by adding nucleotides.
A primer is a nucleic acid strand (or related molecule) that serves as
a starting point for DNA replication
Oka-what? Another Look at Okazaki Fragments.
As you have already learned, the two strands of DNA are antiparallel.
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Replication Blood Cells E. Coli Strand Coding Fragment Molecule Microorganisms Primer Flora
This presents real difficulties during replication. The DNA polymerase
III enzyme synthesizes most of the DNA. The enzyme has two subunits
because both strands of parental DNA must be replicated in the same
place at the same time.
Because DNA can only be synthesized in the 5' to 3' direction, one of
the strands (the 3' to 5' strand) can be copied continuously and is
called the leading strand, while the other, the lagging strand, is
synthesized in fragments so that the 5' to 3' polymerization leads to
overall growth in the 3' to 5' direction. This may be accomplished by
a looping of the template for the lagging strand (see Figure below).
The lagging strand would then pass through the polymerase site in the
same direction as the leading-strand template in the other subunit.
DNA polymerase III would then have to let go of the lagging strand
template (after about 1,000 nucleotides have been added to the lagging
strand). A new loop would then be formed. The gaps between fragments
of the lagging strand are filled by another polymerase, DNA polymerase
I, and the enzyme DNA ligase joins the fragments.
The looping of the template for the lagging strand enables the DNA
polymerase III enzyme (colored yellow) at the replication fork to
synthesize both daughter strands in the 5' to 3' direction. The
leading strand is shown in blue, the lagging strand in green.
[IMAGE]This figure (at left, click to enlarge) may help explain why
the lagging strand must be looped during DNA synthesis. A key point is
that DNA polymerase III in the replication fork is organized into a
dimer - a pair of molecules linked together. Both DNA polymerases
(pink structures in the diagram) are oriented in the same direction
and, as you know, will move along the parent strand from the 3' end to
the 5' end, synthesizing new DNA in the 5' to 3' direction. The purple
ring in the diagram is DnaB helicase, an enzyme that is linked to the
DNA polymerase dimer and functions in separating (unwinding) the two
parent strands from each other. As helicase moves (relative to the
DNA) along, it opens up the replication fork, allowing the polymerases
to access the template strands. Since the polymerases are reading the
templates from right to left in the diagram, the only way for the
bottom template strand to pass through the polymerase in the required
3' to 5' direction is to loop the DNA strand as shown.Upon completion
of one Okazaki fragment the polymerase release that fragment and the
DNA strand is pulled forward bringing the next primed region (green)
into contact with the polymerase and allowing synthesis of a new
fragment to begin.
Frameshift mutation: A deletion or insertion of any number of bases
other than a multiple of three bases has a much more profound effect.
Such frameshift mutation result in a complete change in the amino acid
sequence downstream from the point of mutation, instead of simply a
change in the number of amino acids. (Figure 1)
THE BIG RED DOG RAN OUT.
THE BIG RAD DOG RAN OUT.
THE BIG RED.
Frameshift -- deletion
THE BRE DDO GRA.
Frameshift -- insertion
THE BIG RED ZDO GRA
Causes of mutations: Mutations are caused by substances that disrupt
the chemical structure of DNA or the sequence of its bases.
Radiation, various chemicals, and chromosome rearrangements are some
of the many sources of mutation.
Mutation rates: All of us are subjected to mutagenic events
throughout our lifetime. Depending upon the type of mutation, the
frequency ranges from 10-2/cell division to 10-10/cell division. Our
cells have numerous mechanisms to repair and/or prevent the
propagation of these mutations.
Another type of mutation involves either the insertion or deletion of
one or more (some number that is not a multiple of three) nucleotides
into a DNA sequence. This type of mutation is known as a frameshift
mutation. For an illustration of how devastating this type of
mutation can be if it occurs in the coding region of a gene, delete
the w from the sentence below.
The cow jumped over the moon.
The coj umpedo vert hem oon.
The insertion of nucleotides in multiples of three, if not corrected
during the culling of introns from messenger RNA, will cause the
insertion of an extra amino acid for each three additional
nucleotides. Trinucleotide repeats are a sequence of three
nucleotides that repeat in tandem and vary in the the number of
repeats. Trinucleotide repeat mutations are known to cause at least
eight genetic disorders affecting the nervous or neuromuscular
system. For more about this topic see
YAP an alu insertion
* If DNA is copied incorrectly by the mRNA and a base is deleted (or
added) it causes all other bases to shift over one and code for
incorrect amino acid sequences after the error.
* Frameshift mutation- mutation in which a single base is added or
deleted from DNA
* Frameshift mutations much worse than point mutation due to
quantity of amino acids affected
* Frameshift Mutations: Additions or deletions of one or more
* May result in "garbage" genes, as the entire amino acid sequence
in the code after the change is devastated.
* Large deletions may remove a single amino acid, or an entire
chunk of chromosome. The most common mutation that causes severe
cystic fibrosis deletes only a single codon.
* Real examples of missense, nonsense, and frameshift mutations:
Hemoglobin mutants and Hemoglobin molecule
A note of caution. These examples show the NON-template DNA sequence
rather than the template DNA sequence as in our previous examples.
This is a standard used by DNA scientists. To get the mRNA codons,
just change the Ts to Us.
* Some genes have repeated base sequences, and the number of these
may increase each generation. These expanding genes are
responsible for increasingly severe cases of muscular dystrophy
(CTG repeats), Huntington disease (CAG repeats), and Fragile X
syndrome (CGG repeats).
Fragile X Syndrome:
6-50 CGG repeats in an unaffected individual
50-200 CGG repeats in a carrier
>200 CGG repeats in an affected individual
4Mitosis vs Meiosis
Produces body cells(Somatic cells)
Produces sex cells(Gametes)
Daughter cells diploid(2N)
Daughter cells haploid(N)
Two daughter cells produced
Four daughter cells produced
In metaphase chromosomes line up singley
In metaphase I chromosomes line up as homologous pairs(synapsis)
The two double chromosomes are called a tetrad when they are lined up
Crossing over occurs during the formation of the tetrad
One nuclear division
Two nuclear divisions
Produces cells for growth and repair
Produces cells for sexual reproduction
Daughter cells have two sets of chromosomes(pairs)
Daughter cells have only one member of each pair of chromosomes
Daughter cells are genetically identical to the parent cell
Daughter cells have one-half of the genes from the parent cell
Insures that all daughter cells are genetically identical
Generates genetic diversity through crossing over and ramdom
seperation of homologous pairs of chromosomes
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