BIOLOGY
YEAR 1
QUARTER 2
2018/2019
Molecular Biology and
Recombinant DNA
SUMMARY OF THE COURSE MOLECULAR BIOLOGY AND
RECOMBINANT DNA
NWI-BP010C
ELISE REUVEKAMP
,Content
DNA structure .......................................................................................................................................... 2
DNA replication ....................................................................................................................................... 6
Plasmids ................................................................................................................................................. 10
RNA metabolism .................................................................................................................................... 14
Protein synthesis ................................................................................................................................... 17
Regulation ............................................................................................................................................. 20
, Molecular Biology and recombinant DNA
DNA structure
DNA structure
DNA is made from nucleotides consisting of: Phosphate, Pentose and a Base. The pentose in DNA is
Deoxyribose, meaning that at the 2’ carbon atom binds to an hydroxyl atom, for RNA this is an OH
group and therefore the pentose is called a Ribose.
In water there are 5 tautomer’s of D-ribose enantiomer, but in RNA and DNA
only the β-D-furanose ring is found.
Also in a solution the linear chain (aldehyde) and the ring form (β-furanose)
together form an equilibrium, but again we only find the ring form is found in
DNA and RNA as well.
As you notice there are 5 carbon atoms, of which one is exocyclic. The ring can adopt an ‘envelope’
conformation, having a pucker. In this case 4 of the 5 atoms in the ring are located on the same plane
and the 5th atom can stick out. This can either be on the same plane of the exocyclic carbon atom
(endo) or opposite of the exocyclic carbon atom (exo). In DNA polymers, the C2’of C3’ atoms can be
the puckers.
→ insight to realize that the double stranded B-DNA model should be built using C2’ pucker endo
forms of the furanose ring, another insight is that in dsRNA the C2’ endo pucker causes a conflict
between the phosphate and the 2’OH group, which is not present in deoxy-ribose
Base structures
The glycosyl bond links the pentose ring to the base (pyrimidines
or purines). In the case of pyrimidines it links to the N1 atom and
to the N9 of purines. Also the base could form a syn,- or anti-
conformation, of which the anti-conformation is most likely to
occur.
Pyrimidines are the smaller base structures, as they only contain the cyclic pyrimidine. Purines are
the larger base structures that have a
cyclic pyrimidine and a imidazole.
Adenine, Guanine, Cytosine, Uracil
and Thymine are the 5 bases that we
know form the bases of DNA.
Adenine and Guanine are purines
and the other 3 are pyrimidines, see
the picture below. Exocyclic CH3, OH
and NH2 distinguish the bases.
Transition mutations are mutations in which pyrimidines go from the one structure to another
pyrimidine structure, and also for purines. Transversion is a mutation that occurs in the bases that go
from pyrimidine to purine and vice versa.
YEAR 1
QUARTER 2
2018/2019
Molecular Biology and
Recombinant DNA
SUMMARY OF THE COURSE MOLECULAR BIOLOGY AND
RECOMBINANT DNA
NWI-BP010C
ELISE REUVEKAMP
,Content
DNA structure .......................................................................................................................................... 2
DNA replication ....................................................................................................................................... 6
Plasmids ................................................................................................................................................. 10
RNA metabolism .................................................................................................................................... 14
Protein synthesis ................................................................................................................................... 17
Regulation ............................................................................................................................................. 20
, Molecular Biology and recombinant DNA
DNA structure
DNA structure
DNA is made from nucleotides consisting of: Phosphate, Pentose and a Base. The pentose in DNA is
Deoxyribose, meaning that at the 2’ carbon atom binds to an hydroxyl atom, for RNA this is an OH
group and therefore the pentose is called a Ribose.
In water there are 5 tautomer’s of D-ribose enantiomer, but in RNA and DNA
only the β-D-furanose ring is found.
Also in a solution the linear chain (aldehyde) and the ring form (β-furanose)
together form an equilibrium, but again we only find the ring form is found in
DNA and RNA as well.
As you notice there are 5 carbon atoms, of which one is exocyclic. The ring can adopt an ‘envelope’
conformation, having a pucker. In this case 4 of the 5 atoms in the ring are located on the same plane
and the 5th atom can stick out. This can either be on the same plane of the exocyclic carbon atom
(endo) or opposite of the exocyclic carbon atom (exo). In DNA polymers, the C2’of C3’ atoms can be
the puckers.
→ insight to realize that the double stranded B-DNA model should be built using C2’ pucker endo
forms of the furanose ring, another insight is that in dsRNA the C2’ endo pucker causes a conflict
between the phosphate and the 2’OH group, which is not present in deoxy-ribose
Base structures
The glycosyl bond links the pentose ring to the base (pyrimidines
or purines). In the case of pyrimidines it links to the N1 atom and
to the N9 of purines. Also the base could form a syn,- or anti-
conformation, of which the anti-conformation is most likely to
occur.
Pyrimidines are the smaller base structures, as they only contain the cyclic pyrimidine. Purines are
the larger base structures that have a
cyclic pyrimidine and a imidazole.
Adenine, Guanine, Cytosine, Uracil
and Thymine are the 5 bases that we
know form the bases of DNA.
Adenine and Guanine are purines
and the other 3 are pyrimidines, see
the picture below. Exocyclic CH3, OH
and NH2 distinguish the bases.
Transition mutations are mutations in which pyrimidines go from the one structure to another
pyrimidine structure, and also for purines. Transversion is a mutation that occurs in the bases that go
from pyrimidine to purine and vice versa.
