Lecture 1 BBS1001 – DNA structure and replication
Heterochromatin: high density DNA in nucleus
Euchromatin: low density DNA in nucleus -> more open for transcription
DNA is a double helix built of the following atoms: C,H,O,N,P
Structure:
A&T -> 2 bonds G&C -> 3 bonds
Which means that AT bonds are easier to break and are more often found in places of the DNA
where the strands need to split.
Nitrogen bases:
Binding is always between a purine and a pyrimidine
,Nitrogen bases are attached to the first carbon of a pentose sugar (5 carbon-atoms), in DNA this is D-
2-deoxyribose, in RNA this is D-ribose.
On the fifth carbon, the phosphate group is bound (CH2 group). The sugar group, nitrogen base and
phosphate together form a nucleotide. When there is only a base and a sugar present, it is called a
nucleoside.
When we link nucleotides together, we need a triphosphate which links the nucleotides by a
phoshpdiester linkage. Two phosphate groups from the triphosphate are then deattached which
provides the energy that is needed to create the phosphodiester linkage. The 5’ carbon of the sugar
is attached to the 3’ carbon of the sugar of the other nucleotide.
(RNA contains uracil because it is more stable and RNA has to move outside the cell)
,DNA needs to fit in our cells, this is possible due supercoiling (prokaryotes) and histones
(eukaryotes).
Prokaryotes: don’t have a nucleus and only has one circular molecule of DNA which is all coding DNA.
There are two types of supercoiling: negative and positive. Negative supercoiling means the DNA is
turned negative so that there’s one turn less in the DNA. DNA has a certain tension in which it
remains its form, when you change the structure, tension will build up and the DNA will wrap around
itself to release the tension. Because of the DNA wraps around itself, it will contain the same amount
of turns as it did before but the DNA will be shorter.
In positive supercoiling a turn is added to the DNA, which causes the DNA to tension up which the
DNA wants to get rid of. The DNA will wrap around itself to remove the tension and the extra turn,
making the DNA shorter like in negative supercoiling.
The enzymes who are responsible for adding and removing supercoils are called topoisomerases.
There are two different types: type I (SSB) and type II (DSB). Type I only creates a single break, type II
will make a double strand break (both strands).
, Eukaryotes:
After the supercoiling (also happens in eukaryotes), the DNA will be made more compact with the
help of histones. Histones are proteins which will form a octamere, a core of 8 histone molecules (2
sets of 4) which the DNA will be wrapped around. There are 4 different histones in the histone core
(H2A, H2B, H3 and H4)(140bp), histone H1 is used to keep the complex together and is called the
spacer (60bp). The DNA is wrapped around the histone complex 2 times, which contains around 200
basepairs. Each complex of DNA with its histones is called a nucleosome.
The nucleosomes (which look like beads on a string) are then wrapped around each other again to
form a structure called solenoid this is the structure of chromatin. The histones are positively
charged while the DNA is negatively charged which is why there is a strong attraction between the
DNA and the histones.
To even compact the DNA further, non-histone proteins are needed. The DNA will form loops trough
the non-histone proteins. This will form a 2D flower-like structure, which can be added behind each
other to form a chromosome.
The chromosomes consist of arms called chromatids, these are kept together by the centromere.
We have a short arm (p arm) and a long arm (q arm).
Heterochromatin: high density DNA in nucleus
Euchromatin: low density DNA in nucleus -> more open for transcription
DNA is a double helix built of the following atoms: C,H,O,N,P
Structure:
A&T -> 2 bonds G&C -> 3 bonds
Which means that AT bonds are easier to break and are more often found in places of the DNA
where the strands need to split.
Nitrogen bases:
Binding is always between a purine and a pyrimidine
,Nitrogen bases are attached to the first carbon of a pentose sugar (5 carbon-atoms), in DNA this is D-
2-deoxyribose, in RNA this is D-ribose.
On the fifth carbon, the phosphate group is bound (CH2 group). The sugar group, nitrogen base and
phosphate together form a nucleotide. When there is only a base and a sugar present, it is called a
nucleoside.
When we link nucleotides together, we need a triphosphate which links the nucleotides by a
phoshpdiester linkage. Two phosphate groups from the triphosphate are then deattached which
provides the energy that is needed to create the phosphodiester linkage. The 5’ carbon of the sugar
is attached to the 3’ carbon of the sugar of the other nucleotide.
(RNA contains uracil because it is more stable and RNA has to move outside the cell)
,DNA needs to fit in our cells, this is possible due supercoiling (prokaryotes) and histones
(eukaryotes).
Prokaryotes: don’t have a nucleus and only has one circular molecule of DNA which is all coding DNA.
There are two types of supercoiling: negative and positive. Negative supercoiling means the DNA is
turned negative so that there’s one turn less in the DNA. DNA has a certain tension in which it
remains its form, when you change the structure, tension will build up and the DNA will wrap around
itself to release the tension. Because of the DNA wraps around itself, it will contain the same amount
of turns as it did before but the DNA will be shorter.
In positive supercoiling a turn is added to the DNA, which causes the DNA to tension up which the
DNA wants to get rid of. The DNA will wrap around itself to remove the tension and the extra turn,
making the DNA shorter like in negative supercoiling.
The enzymes who are responsible for adding and removing supercoils are called topoisomerases.
There are two different types: type I (SSB) and type II (DSB). Type I only creates a single break, type II
will make a double strand break (both strands).
, Eukaryotes:
After the supercoiling (also happens in eukaryotes), the DNA will be made more compact with the
help of histones. Histones are proteins which will form a octamere, a core of 8 histone molecules (2
sets of 4) which the DNA will be wrapped around. There are 4 different histones in the histone core
(H2A, H2B, H3 and H4)(140bp), histone H1 is used to keep the complex together and is called the
spacer (60bp). The DNA is wrapped around the histone complex 2 times, which contains around 200
basepairs. Each complex of DNA with its histones is called a nucleosome.
The nucleosomes (which look like beads on a string) are then wrapped around each other again to
form a structure called solenoid this is the structure of chromatin. The histones are positively
charged while the DNA is negatively charged which is why there is a strong attraction between the
DNA and the histones.
To even compact the DNA further, non-histone proteins are needed. The DNA will form loops trough
the non-histone proteins. This will form a 2D flower-like structure, which can be added behind each
other to form a chromosome.
The chromosomes consist of arms called chromatids, these are kept together by the centromere.
We have a short arm (p arm) and a long arm (q arm).
