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Study guide for DNA and replication
Definition:
1. Double helix: the form of native DNA, referring to its two adjacent polynucleotide strands wound into a
spiral shape; basically, the twisted ladder structure of DNA.
2. Nucleotide: an organic monomer consisting of a
five-carbons sugar covalently bonded to a nitrogenous
base and a phosphate group. Nucleotide are the
building blocks of nucleic acids.
3. Deoxyribose: a sugar derived from ribose by
replacing a hydroxyl group with hydrogen
4. Nitrogenous base: a nitrogen-containing molecule
that has the same chemical properties as a base.
5. Adenine: a double ring nitrogenous base found in
DNA and RNA
6. Guanine: a double ring nitrogenous base found in
DNA and RNA
7. Cytosine: a single ring nitrogenous base found in
DNA and RNA
8. Thymine: a single ring nitrogenous base found in DNA and RNA
9. Antiparallel: a term applied to two molecules that are side by side but run in opposite directions. The
two strands of DNA are antiparallel. The head of one strand is always laid against the tail of the other strand
of DNA.
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10. 5 prime: indicate the carbon numbers in the DNA's sugar backbone. The 5' carbon has a phosphate
group attached to it.
11. 3 prime: indicate the carbon numbers in the DNA's sugar backbone. The 3' carbon has a hydroxyl (-OH)
group attached to it.
12. Helicase: an enzyme that unwinds the DNA by breaking the hydrogen bonds that keeps them together.
13.
Endonuclease: an enzyme which cleaves a
polynucleotide chain by separating nucleotides other
than the two end ones.
14.
Exonuclease: an enzyme which removes
successive nucleotides from the end of a
polynucleotide molecule.
15.
DNA polymerase: is an enzyme that is
responsible for creating new strands of DNA, by
assembling nucleotides, the building blocks of
DNA
16. Leading strand: the template strand of the
DNA double helix that is oriented so that the
replication fork moves along it in the 3' to 5'
direction.
17. Lagging strand: the strand of the template DNA double helix that is oriented so that the replication fork
moves along it in a 5' to 3' manner
18. Okazaki fragment: short sequences of DNA nucleotides which are synthesized discontinuously and
later linked together by the enzyme DNA ligase to create the lagging strand during DNA replication.
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Essay
DNA function
DNA stands for Deoxyribonucleic Acid. As the crash course video puts it, DNA is the 6 billion letter code
which provides the assembly instructions for everything that you are. In proper words, DNA is a nucleic acid
that contains the genetic instructions for the development and function of living things. What DNA is for is just
storing that information. DNA also hold other components of the cell like RNA and protein molecules. Also,
DNA does not act directly on other molecule but let enzymes act on DNA to replicate the DNA or transcribe
into protein.
DNA structure
Chromosome > Telomere > Nucleosome (histone + DNA) > DNA as double helix
“DNA is a long polymer of simple units called nucleotides.” Individual nucleotide is made up of a 5 carbon
sugar molecule called deoxyribose, a phosphate group, and one of the four nitrogenous group. The 4
nitrogenous bases are Adenine (A), Thymine (T), Cytosine (C), Guanine (G). Adenine and Guanine are
double ring while Thymine and Cytosine are single ring nitrogen bases. One of the nitrogen base can only pair
one another nitrogen base and that pair is called a base pair. Adenine always pairs with Thymine by 2 hydrogen
bonds and Cytosine always bonds with Guanine by 3 hydrogen bonds making this base pair slightly stronger.
One of the polynucleotide is attached to another polynucleotide by the nitrogen bases. They are places next to
each other but go in opposite direction. The first polynucleotide runs in 5’ to 3’ direction while the other
polynucleotide runs in 3’ to 5’ direction. 5 prime (5’) is the 5th carbon of the sugar attached to phosphate group
while 3 prime (3’) is the 3rd carbon of sugar attached to phosphate group. So, the diagrams of DNA seem to
have polynucleotides running in opposite direction. That is why they are called antiparallel. This forms a
ladder with nitrogen bases as the stairs and sugar and phosphate group as the rails of the ladder. Upon this, the
ladder is twisted into the double helix shape.
DNA Replication
DNA is replicated by using half of the original DNA as a templet. In the first step, an enzyme called helicase
unwinds the DNA double helix by breaking down the hydrogen bonds between the nitrogen bases to make the it
into two separate strands of polynucleotide. The strand that run in 3’ to 5’ direction is called leading strand
while the strand that runs in 5’ to 3’ direction is called lagging strand. In the leading strand RNA primase starts
the strand with a set of primer and is only used once. Then, DNA polymerase 3, an enzyme continues through
strand and keep adding the complementary nucleotides to the original leading strand all the way down. Note
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that DNA polymerase can only work in 5’ to 3’ direction. So, in lagging strand the replication is done in
segments. First RNA primase puts down the primer and then DNA polymerase goes backward along the strand.
This means that DNA polymerase goes in the opposite direction of DNA unwinding site. The RNA primase
again puts some set of primers and DNA polymerase put the nucleotides and the process repeats until a whole
new DNA strand is completed from the lagging strand. These segments of DNA made in discontinuous process
are called Okazaki fragment. Then another kind of DNA polymerase called DNA polymerase 1 goes through
the strand to replace all the primers from RNA primase. In the end, DNA ligase, an enzyme that connects the
Okazaki fragments by forming a bond between the phosphate group and the deoxyribose group goes through the
lagging strand. All these processes make two new DNA using half of the original DNA as one of the strand.
Endonuclease is an enzyme that breaks down the bond between phosphate group and sugar. The purpose can
vary, but the main purpose of endonuclease is to help in repairing the DNA to avoid mutation. Endonuclease
usually breaks at specific site like at 4-6 codes that are palindromic. Restriction endonucleases breaks the bond
only at very specific nucleotide sequence in the DNA. Some endonuclease breaks down to add methyl to DNA
with methylase if there are viral DNA in the nucleus. It can help to recognize which is your DNA versus which
one is viral DNA.
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