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DNA Structure
- Just as amino acids are the monomers of proteins, nucleotides are the monomers of
nucleic acid
- ​Chargaff’s Rule:​ the ratio of pyrimidines: purines should be 1:1 (A:T = 1:1; C:G = 1:1)
- Nucleic acids are made up of ​PONCHO​ (thanks Mr. Grimm!) while proteins are full of
CHNOS
- Pyrimidines: single-ringed nucleotides. Think ​CUT P​ie, or cytosine, uracil, thymine and
pie-rymidine
- Purines: double-ringed fatties/nucleotides. Think of ​GAP ​jeans, or guanine, adenine,
pur-jeans/purines
- Adenine will form three hydrogen bonds with thymine/uracil; cytosine will form two
hydrogen bonds with guanine
- The backbone is made up of alternating sugars (deoxyribose or ribose) and phosphates
that are joined by covalent phosphodiester bonds
- DNA is ​antiparallel, ​meaning that its two strands run opposite of each other.
1) 5’ → 3’: will be the lagging strand because
it is in the opposite direction that DNA pol III
reads.
2) 3’ → 5’: will be the leading strand because
it is in the direction DNA polymerase III reads
3) The 5’ end will be the end with a phosphate
group while the 3’ will be the end with the sugar.
4) The names come from the nomenclature
(naming system) of sugars. The 3’ end is what it is
because the 3’ carbon is free and not bound to a
phosphate.
How it all comes together
- Nucleotides, in their lonely, single forms, have a
triphosphate tail that is rich in potential energy
- e.g.: in DNA: dATP (free form) → dAMP (in DNA); dGTP →
dGMP; dCTP → dCMP; dTTP → dTMP
- “d” means “deoxy,” which differentiates the
nucleotide from being a monomer for DNA versus RNA.
- The nucleotides differ in that deoxyribose is one
oxygen atom short of being ribose.
- e.g.: in RNA: ATP → AMP; GTP → GMP; CTP → CMP; UTP
→UMP
- Energy​ coupling: The exergonic ​dephosphorylation of
nucleotides fuels the endergonic reaction of ​building
covalent bonds between nucleotides and the
sugar-phosphate backbone (phosphodiester bonds)
OR: dephosphorylation → build covalent bonds
- What builds them? DNA pol III!
​
DNA Replication
- Cells need to divide in order to reproduce, so what happens to their DNA as
they divide? It has already divided and prepared for binary fission/asexual
reproduction through DNA replication during the ​S phase​, or DNA ​s​ynthesis phase
of its life cycle.
- Replication begins at the ​ORI​, or origin of replication
1) ​Helicase​ unzips the dress ;) to reveal the ​antiparallel​ strands of DNA: one goes 3’
to 5’ while the other goes 5’ to 3’
a) since helicase is going ​up the dress, the orange side will be the leading
strand since you will be going in the 3’ → 5’ direction which is easier for DNA
polymerase III to follow
b) helicase splits the double stranded DNA by breaking the hydrogen bonds
between nucleotides
2) ​Topoisomerase​ keeps the strands from twisting together
3)​ ​Single-stranded DNA binding proteins​ keep the DNA strands from rebinding to
each other
4) ​RNA primase​ synthesizes a section of complementary RNA/​RNA primers​ that
forms a section of dsDNA/double-stranded DNA that ​DNA pol III​ can attach to.
a) The primers are identifiable by their unique nucleotide (uracil)
b) Required for replication of ​both​ leading and lagging strands to occur
c) RNA primers are on both leading & lagging strands but more often on
the lagging strand
5) DNA polymerase III begins to replicate both the leading and lagging strands:
a) The ​leading strand​ is easily replicated since it runs 3’ → 5’, which is the direction
DNA pol III reads. The replicated strand, however, runs 5’ → 3’ since it is a copied
strand.
b) The ​lagging strand​ is not as easily replicated since it runs 5’ → 3’, which is opposite of the direction DNA pol III. To
accommodate for this, RNA primase makes multiple primers for DNA pol III to hop onto and follow to form ​Okazaki
fragments​.
Note: DNA pol III follows the replication fork on the leading strand, but it goes in the opposite direction on the
lagging strand because of DNA’s antiparallel structure
5) ​DNA polymerase I​ eats up the RNA primers (cuz you don’t want RNA in your DNA!)
6) ​Ligase​ binds the Okazaki fragments together to form a cohesive lagging strand.
Note:
- The purple asterisk (next the bottom right ligase) is signifying another DNA pol III that should be there as it would be forming the
leading strand.
- The replication fork goes both ways because the ORI/origin of replication splits the DNA strands into two parts: a 5’ → 3’ strand and a
3’ → 5’ strand. Therefore, on opposite sides of the ORI, there will be a leading and lagging strand ​depending on the direction of the
replication fork and strand orientation. DNA pol III will always read 3’ → 5’ and build 5’ → 3’, though.
-
DNA pol III ​needs​ a primer to form a section of dsDNA that it can begin DNA replication on (not shown, oops)
Another visual aid:
Bibliography:
1) Nucleotides and sugar-phosphate backbone:
http://www.phschool.com/science/biology_place/biocoach/bioprop/images/dnachem2.gif
2) DNA structure:
https://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&ved=0ahUKEwi3qp_jjL7SAhVB4CYKHW7HCuAQjBwIBA&
url=http%3A%2F%2Fwww.compoundchem.com%2Fwp-content%2Fuploads%2F2015%2F03%2FChemical-structure-of-DNA.png&p
sig=AFQjCNGjNoBFHCgEmPUOT0435HFfijDgYg&ust=1488759851610137
3) Deoxyribose v ribose: ​https://www.mun.ca/biology/scarr/iGen3_02-07_Figure-L.jpg