DNA Structure Atomic
Biology:
Molecular biology is about molecules; the
central dogma of molecular biology was
initiated by Francis Crick in 1958; the idea
is that you have DNA, which stores
genetic information. This can be
transcribed to form RNA, which is the
expression of the genetic information.
That RNA can then
serve to make proteins (translation).
DNA vs RNA
DNA Replication
Transcription and Translation
Protein synthesis
Biomolecules
What is ATP?
DNA is made up out of three parts. A sugar, a
phosphate and a base.
Sugar (pentose)
The sugar in DNA is a 5-carbon ring. In a solution,
this sugar oscillates between a ring form and a
linear form. In DNA and RNA
we only find the ring form;
there are several ring forms,
but this one is called the
beta-furanose.
It is a 5 carbon-ring, but the
ring is made up out of only 4 carbons and an oxygen,
with one extra carbon outside of the ring (exocyclic).
RNA has ribose and DNA has Deoxyribose; in DNA the
2” hydroxyl group is missing. (Deoxy = missing one
oxygen).
The numbering in the pentose C’s is done by taking the Oxygen as 0, after
zero the first C is 1” (1 prime), etc. The 5” (5 prime) is the exocyclic
carbon. In general, we say the 5” end of the DNA is the beginning, and the
3” end is the end.
In the bases there are also carbons, but they do not get a prime; so the
prime distinguishes the pentose carbons from the base carbons.
Pentose puckering
A cyclic structure is not flat. In pentose, one of
the corners (either C-2” or C-3”) can ‘pucker’.
Four of the five atoms are then located on the
same plane, and the 5th lies on the same (endo)
,or the opposite (exo) side of the C-5” exocylic arm.
In B-DNA, the C-2” will form an endo pucker. In RNA and A-DNA, the C-3”
will endo pucker.
In double strand RNA, the C-2” endo pucker causes a steric conflict
between the phosphate and the 2’OH group, which is absent in DNA. This
is why dsRNA adopts other geometries than B-DNA, namely a structure
that is related to the A-DNA double helix.
DNA is an acid. It is therefor best soluble in basic (alkaline) solutions. If
you want to purify DNA and get it out of a solution, you can acidify.
Another thing you can do is remove the water; you do that by adding
ethanol. The concentration of water decreases, the hydration of DNA
decreases, and DNA starts to form crystals which are precipitates.
Cyanide (CNH) is a dangerous compound, but if
you take 5 cyanide molecules, it will spontaneously
form Adenine. There is a lot of cyanide in outer
space, which forms adenine. It does not contain
any oxygen.
Bases
The bases of DNA are heterocyclic molecules (C+N). A heterocyclic
molecule is a cyclic molecule with different atoms in its ring.
Bases are lightly alkaline (pH > 7), aromatic (double bonds) and
hydrophobic.
We distinguish two different types of these bases. Pyrimidines (small) and
purines (big). The archetypical purine and pyrimidine bases lack oxygen.
In DNA we find 4 different bases:
Adenine, Thymine, Guanine and
Cytosine.
In RNA we find Uracil instead of
Thymine.
Adenine is a purine without any
oxygen.
Guanine is a purine with an
oxygen and an extra NH₂ group.
Cytosine is a pyrimidine with one
oxygen and a NH₂ group.
Uracil is a pyrimidine with two
oxygen.
Thymine is Uracil with an
exocyclic CH₃.
Inosene is deaminated Adenine and
bound to a sugar.
Adenine and Thymine are bound together by 2 hydrogen bonds. Cytosine
and Guanine are bound together by 3 hydrogen bonds.
The rules of Chargaff
, Because in DNA all Adenines (Purine) are coupled with Thymines
(Pyrimidines), and Guanine and Cytosine are coupled, the number of
purines and pyrimidines in DNA is equal. (Not RNA).
The ratio of A to T and G to C are equal to 1. [dA] = [dT], [dG] =
[dC].
Organisms differ in ratio A+T / G + C There are species with AT-
rich genomes and other with GC-rich genomes.
[A + T] / [C + G] is constant in the tissues of multi-cellular
organisms.
[A + T] / [C + G] does not change as a function of age.
The bases are attached to the sugars
(pentose) with covalent bonds. This
bond happens on the N1 of Pyrimidines
and on the N9 of Purine, with the C-1”
of the sugar.
A bond to a sugar is called a glycosyl
bond.
In this case it is an N-ß-glycosyl bond,
as it’s connected to a nitrogen.
The glycosyl bond should be
movable but isn’t because
electrophilic interactions. This
leads to either a syn-
conformation, where both the
sugar and base are facing the
same way, or an anti-
conformation, where they are
facing away. Pyrimidines are almost always in the anti-conformation.
Because we are in an
oxygen-rich atmosphere,
oxidation happens. For a
base, that means its
nitrogen gets replaced by
an oxygen. This is also
called deamination.
When adenine is oxidated,
it becomes hypoxanthine;
if this is bound to a sugar
it is called inosine.
When building the DNA model, Watson and Crick had to deal with
electrophilic interactions between molecules; positive and negative
, charges attracting each other.
Something they needed to consider was base tautomerisation.
Tautomers are structural isomers of chemical
compounds that readily interconvert by
relocating a hydrogen atom
or a double bond. These
tautomers can usually not
be purified away from each
other, because they change
very fast. The properties of a chemical are therefore
the average of the properties of the tautomers that are
present. The bases have an enol-form (-OH) and a keto-
form (=O). A key for Watson and Crick was the
realization that the atomic model uses the keto-forms of the bases.
Phosphates
Phosphate (PO₄), like with NH₃+ and CH₄, has a
tetrahedral geometry. This is interesting, because
phosphorus (P) has 5 valencies, but the last free
valency to form a double bond is shared by all the
oxygens.
In nucleotides, the phosphate
is on the C-5” of the sugar.
The other phosphate in the
DNA chain is attached to the
3”-OH group.
You can have
monophosphates (α-
phosphate), diphosphates (an
α-phosphate and a β
phosphate), or triphosphates
(an α-phosphate and a β phosphate and a γ-phosphate)
Nucleotide – nucleoside – base
Nucleobase Adenine
Nitrogen-rich base Cytosine
Guanine
Thymine
Uracil
Nucleoside Adenosine
Nitrogen-rich base Cytidine
+ Pentose sugar Guanosine
Thymidine
Uridine
Nucleotide Adenosine 5’ phosphate (ATP)
Nitrogen-rich base Cytidine 5’ phosphate
+ Pentose sugar Guanosine 5’ phosphate (GTP)
+ Phosphate Thymidine 5’ phosphate
Biology:
Molecular biology is about molecules; the
central dogma of molecular biology was
initiated by Francis Crick in 1958; the idea
is that you have DNA, which stores
genetic information. This can be
transcribed to form RNA, which is the
expression of the genetic information.
That RNA can then
serve to make proteins (translation).
DNA vs RNA
DNA Replication
Transcription and Translation
Protein synthesis
Biomolecules
What is ATP?
DNA is made up out of three parts. A sugar, a
phosphate and a base.
Sugar (pentose)
The sugar in DNA is a 5-carbon ring. In a solution,
this sugar oscillates between a ring form and a
linear form. In DNA and RNA
we only find the ring form;
there are several ring forms,
but this one is called the
beta-furanose.
It is a 5 carbon-ring, but the
ring is made up out of only 4 carbons and an oxygen,
with one extra carbon outside of the ring (exocyclic).
RNA has ribose and DNA has Deoxyribose; in DNA the
2” hydroxyl group is missing. (Deoxy = missing one
oxygen).
The numbering in the pentose C’s is done by taking the Oxygen as 0, after
zero the first C is 1” (1 prime), etc. The 5” (5 prime) is the exocyclic
carbon. In general, we say the 5” end of the DNA is the beginning, and the
3” end is the end.
In the bases there are also carbons, but they do not get a prime; so the
prime distinguishes the pentose carbons from the base carbons.
Pentose puckering
A cyclic structure is not flat. In pentose, one of
the corners (either C-2” or C-3”) can ‘pucker’.
Four of the five atoms are then located on the
same plane, and the 5th lies on the same (endo)
,or the opposite (exo) side of the C-5” exocylic arm.
In B-DNA, the C-2” will form an endo pucker. In RNA and A-DNA, the C-3”
will endo pucker.
In double strand RNA, the C-2” endo pucker causes a steric conflict
between the phosphate and the 2’OH group, which is absent in DNA. This
is why dsRNA adopts other geometries than B-DNA, namely a structure
that is related to the A-DNA double helix.
DNA is an acid. It is therefor best soluble in basic (alkaline) solutions. If
you want to purify DNA and get it out of a solution, you can acidify.
Another thing you can do is remove the water; you do that by adding
ethanol. The concentration of water decreases, the hydration of DNA
decreases, and DNA starts to form crystals which are precipitates.
Cyanide (CNH) is a dangerous compound, but if
you take 5 cyanide molecules, it will spontaneously
form Adenine. There is a lot of cyanide in outer
space, which forms adenine. It does not contain
any oxygen.
Bases
The bases of DNA are heterocyclic molecules (C+N). A heterocyclic
molecule is a cyclic molecule with different atoms in its ring.
Bases are lightly alkaline (pH > 7), aromatic (double bonds) and
hydrophobic.
We distinguish two different types of these bases. Pyrimidines (small) and
purines (big). The archetypical purine and pyrimidine bases lack oxygen.
In DNA we find 4 different bases:
Adenine, Thymine, Guanine and
Cytosine.
In RNA we find Uracil instead of
Thymine.
Adenine is a purine without any
oxygen.
Guanine is a purine with an
oxygen and an extra NH₂ group.
Cytosine is a pyrimidine with one
oxygen and a NH₂ group.
Uracil is a pyrimidine with two
oxygen.
Thymine is Uracil with an
exocyclic CH₃.
Inosene is deaminated Adenine and
bound to a sugar.
Adenine and Thymine are bound together by 2 hydrogen bonds. Cytosine
and Guanine are bound together by 3 hydrogen bonds.
The rules of Chargaff
, Because in DNA all Adenines (Purine) are coupled with Thymines
(Pyrimidines), and Guanine and Cytosine are coupled, the number of
purines and pyrimidines in DNA is equal. (Not RNA).
The ratio of A to T and G to C are equal to 1. [dA] = [dT], [dG] =
[dC].
Organisms differ in ratio A+T / G + C There are species with AT-
rich genomes and other with GC-rich genomes.
[A + T] / [C + G] is constant in the tissues of multi-cellular
organisms.
[A + T] / [C + G] does not change as a function of age.
The bases are attached to the sugars
(pentose) with covalent bonds. This
bond happens on the N1 of Pyrimidines
and on the N9 of Purine, with the C-1”
of the sugar.
A bond to a sugar is called a glycosyl
bond.
In this case it is an N-ß-glycosyl bond,
as it’s connected to a nitrogen.
The glycosyl bond should be
movable but isn’t because
electrophilic interactions. This
leads to either a syn-
conformation, where both the
sugar and base are facing the
same way, or an anti-
conformation, where they are
facing away. Pyrimidines are almost always in the anti-conformation.
Because we are in an
oxygen-rich atmosphere,
oxidation happens. For a
base, that means its
nitrogen gets replaced by
an oxygen. This is also
called deamination.
When adenine is oxidated,
it becomes hypoxanthine;
if this is bound to a sugar
it is called inosine.
When building the DNA model, Watson and Crick had to deal with
electrophilic interactions between molecules; positive and negative
, charges attracting each other.
Something they needed to consider was base tautomerisation.
Tautomers are structural isomers of chemical
compounds that readily interconvert by
relocating a hydrogen atom
or a double bond. These
tautomers can usually not
be purified away from each
other, because they change
very fast. The properties of a chemical are therefore
the average of the properties of the tautomers that are
present. The bases have an enol-form (-OH) and a keto-
form (=O). A key for Watson and Crick was the
realization that the atomic model uses the keto-forms of the bases.
Phosphates
Phosphate (PO₄), like with NH₃+ and CH₄, has a
tetrahedral geometry. This is interesting, because
phosphorus (P) has 5 valencies, but the last free
valency to form a double bond is shared by all the
oxygens.
In nucleotides, the phosphate
is on the C-5” of the sugar.
The other phosphate in the
DNA chain is attached to the
3”-OH group.
You can have
monophosphates (α-
phosphate), diphosphates (an
α-phosphate and a β
phosphate), or triphosphates
(an α-phosphate and a β phosphate and a γ-phosphate)
Nucleotide – nucleoside – base
Nucleobase Adenine
Nitrogen-rich base Cytosine
Guanine
Thymine
Uracil
Nucleoside Adenosine
Nitrogen-rich base Cytidine
+ Pentose sugar Guanosine
Thymidine
Uridine
Nucleotide Adenosine 5’ phosphate (ATP)
Nitrogen-rich base Cytidine 5’ phosphate
+ Pentose sugar Guanosine 5’ phosphate (GTP)
+ Phosphate Thymidine 5’ phosphate
