Case 2
Learning goals
What is DNA
Structure (how they are represented),
Primary: DNA is formed out of alternating deoxyribose (sugar, C5H10O4) and
phosphate (PO4-) groups. Each phosphate group is linked to the 3’ carbon of
one deoxyribose unit and to the 5’ carbon of the next deoxyribose unit.
The sugar forms a phosphate ester at the 3’
and 5’ position. An ester is chemical binding
in which an -OH is replaced by an -O-alkyl
group
Secondary: In the DNA double
helix, the two polynucleotide
chains run in opposite
directions (which is called
antiparallel).
At each end of the double helix, there is
one 5’ OH and one 3’ OH. The sugar–
phosphate backbone is on
the outside and the bases point inward.
The form of the DNA double helix called B-DNA
A nucleotide is a phosphate, deoxyribose
A-form, B-form and Z-form DNA
The B-form is the most common found DNA form. A- and B- are both right-
handed, but the Z-form is left-handed. A-DNA is compressed and broader than
B-DNA and is formed by dehydration.
Together with histones, DNA forms a nucleosome. Several nucleosomes
form a chromatin, whose primary function is packaging long DNA molecules
into more compact, denser structures. This prevents the strands from
becoming tangled and also plays important roles in reinforcing the DNA during
cell division, preventing DNA damage, and regulating gene expression and
DNA replication.
Function,
DNA consists of codons. The coding sequences are called exons, the
noncoding sequences are called introns. The bases (A, C, G, T) that are
linked, one to each sugar unit, are the side chains. They carry all of the
information necessary for protein synthesis. Synthesis is the combination of
components to form a connected whole. So protein synthesis is the process in
which cells produce protein, they do this by transcription and translation.
The function of DNA is reproducing itself and supply information to make RNA
and proteins.
Duplication/replication,
When replication happens, the two
daughter strands are synthesised in
different ways. There is the leading
strand (3’ to 5’) and the lagging strand
, (5’ to 3’). Replication always proceeds from the 5’ to the 3’ direction and
always requires a primer. A primer is a little piece of DNA or RNA which is
used as starting point for the polymerase chain reaction.
It is called semi conservative, because one strand is always old and the
other newly synthesized.
The replication happens in several steps
1. Helicase unzips dna strand.
2. Ssb proteins makes sure strand doesnt close again by binding to the
separated strands
3. DNA polymerase attaches new nucleotide.
4. Subunit of DNA polymerase, DNA polymerase 1, proofreads DNA
using 3’ → 5’ exonuclease activity. When an incorrect base pair is
recognized, DNA polymerase reverses its direction by one base pair of
DNA and excises the mismatched base. Following base excision, the
polymerase can re-insert the correct base and replication can continue.
5. DNA ligase seals strands together.
6. DNA molecule winds up.
The lagging strand uses Okazaki fragments, because it has to be done
in a 5’ to 3’ direction. Okazaki fragments are a little piece of DNA with a
primer. DNA ligase links the ends of two Okazaki fragments together
DNA topoisomerases regulate DNA supercoiling. Type I topoisomerases
change the degree of supercoiling of DNA by causing single-strand breaks
and re-ligation, whereas type II topoisomerases cause double-strand breaks.
It is the task for primase to assemble the first nucleotides of a new chain.
Transcription,
The process in which information encoded in a DNA molecule is copied into
an mRNA molecule
Transcription is the synthesis of mRNA. The transcriptional start sites are
marked by promoter sequences on the DNA, and the first task for the RNA
polymerase is finding the promoter, existing of a TATA box and initiator.
Transcription, just like replication, requires an single-stranded template.
RNA polymerase doesn’t require a
primer.
The template strand is
complementary to the RNA, while
the coding strand has the same
base sequencing as RNA. The
transcription ends with the
terminator.
3 steps of transcription:
Initiation: The RNA polymerase
binds to the promoter. RNA
Polymerase then unwinds the DNA
strands
Elongation: The template strand,
acts as a template for RNA
Learning goals
What is DNA
Structure (how they are represented),
Primary: DNA is formed out of alternating deoxyribose (sugar, C5H10O4) and
phosphate (PO4-) groups. Each phosphate group is linked to the 3’ carbon of
one deoxyribose unit and to the 5’ carbon of the next deoxyribose unit.
The sugar forms a phosphate ester at the 3’
and 5’ position. An ester is chemical binding
in which an -OH is replaced by an -O-alkyl
group
Secondary: In the DNA double
helix, the two polynucleotide
chains run in opposite
directions (which is called
antiparallel).
At each end of the double helix, there is
one 5’ OH and one 3’ OH. The sugar–
phosphate backbone is on
the outside and the bases point inward.
The form of the DNA double helix called B-DNA
A nucleotide is a phosphate, deoxyribose
A-form, B-form and Z-form DNA
The B-form is the most common found DNA form. A- and B- are both right-
handed, but the Z-form is left-handed. A-DNA is compressed and broader than
B-DNA and is formed by dehydration.
Together with histones, DNA forms a nucleosome. Several nucleosomes
form a chromatin, whose primary function is packaging long DNA molecules
into more compact, denser structures. This prevents the strands from
becoming tangled and also plays important roles in reinforcing the DNA during
cell division, preventing DNA damage, and regulating gene expression and
DNA replication.
Function,
DNA consists of codons. The coding sequences are called exons, the
noncoding sequences are called introns. The bases (A, C, G, T) that are
linked, one to each sugar unit, are the side chains. They carry all of the
information necessary for protein synthesis. Synthesis is the combination of
components to form a connected whole. So protein synthesis is the process in
which cells produce protein, they do this by transcription and translation.
The function of DNA is reproducing itself and supply information to make RNA
and proteins.
Duplication/replication,
When replication happens, the two
daughter strands are synthesised in
different ways. There is the leading
strand (3’ to 5’) and the lagging strand
, (5’ to 3’). Replication always proceeds from the 5’ to the 3’ direction and
always requires a primer. A primer is a little piece of DNA or RNA which is
used as starting point for the polymerase chain reaction.
It is called semi conservative, because one strand is always old and the
other newly synthesized.
The replication happens in several steps
1. Helicase unzips dna strand.
2. Ssb proteins makes sure strand doesnt close again by binding to the
separated strands
3. DNA polymerase attaches new nucleotide.
4. Subunit of DNA polymerase, DNA polymerase 1, proofreads DNA
using 3’ → 5’ exonuclease activity. When an incorrect base pair is
recognized, DNA polymerase reverses its direction by one base pair of
DNA and excises the mismatched base. Following base excision, the
polymerase can re-insert the correct base and replication can continue.
5. DNA ligase seals strands together.
6. DNA molecule winds up.
The lagging strand uses Okazaki fragments, because it has to be done
in a 5’ to 3’ direction. Okazaki fragments are a little piece of DNA with a
primer. DNA ligase links the ends of two Okazaki fragments together
DNA topoisomerases regulate DNA supercoiling. Type I topoisomerases
change the degree of supercoiling of DNA by causing single-strand breaks
and re-ligation, whereas type II topoisomerases cause double-strand breaks.
It is the task for primase to assemble the first nucleotides of a new chain.
Transcription,
The process in which information encoded in a DNA molecule is copied into
an mRNA molecule
Transcription is the synthesis of mRNA. The transcriptional start sites are
marked by promoter sequences on the DNA, and the first task for the RNA
polymerase is finding the promoter, existing of a TATA box and initiator.
Transcription, just like replication, requires an single-stranded template.
RNA polymerase doesn’t require a
primer.
The template strand is
complementary to the RNA, while
the coding strand has the same
base sequencing as RNA. The
transcription ends with the
terminator.
3 steps of transcription:
Initiation: The RNA polymerase
binds to the promoter. RNA
Polymerase then unwinds the DNA
strands
Elongation: The template strand,
acts as a template for RNA
