Deep Thought Questions for Mini Test 1
1. How did Reiji Okazaki test if DNA replication was continuous or
discontinuous?
An Okazaki fragment is a short fragment of DNA (with RNA primer on 5’
terminus) which is created on the lagging strand throughout DNA replication.
This was discovered in 1968 by Reiji Okazaki and their colleagues during the
study of replication of bacteriophage DNA in E Coli.
Okazaki reasoned three possibilities for replicating double-stranded DNA. The
continuous model is impossible due to the nature of the polymerases (replication
in one direction). Thus, he needed to demonstrate semi-continuous or
discontinuous. For this, the pulse-labelling technique was used. Bacterial cells
infected with wild type/bacterial virus’ is given radioactively labelled DNA
precursor. With this, using sucrose, DNA molecules do not find their equilibrium
position, so molecules are always in motion. The ultracentrifuge must be stopped
at an experimentally determined time for the experiment to work. Here, DNA
synthesis has taken place during the pulse time producing radiolabeled thymine
located on the gradient.
During very short times of labelling, short pieces of DNA are found, With longer
times, pieces of DNA were increasing longer. Then he used the same experiement
with a defective mutant virus called DNA ligase. This is the enzyme joining
pieces of DNA together in larger structures. These labelled pieces of DNA
remained short, even after radiolabelling for long periods.
Further data suggested that DNA replication occurred by synthesis of small
pieces later linked together by DNA ligase. This was proved by a pulse-chase
experiment. His uninfected bacterial culture was radiolabeled for a short time,
which was followed by adding large excess of unlabelled precursor. The resulted
in a decrease in the quantity of radiolabel incorporated and allowed him to
follow fate of short pieces. The data then reflected that DNA which was labelled
during the 30 second pulse but eventually winds up in large DNA, which is
equivalent to the size of genome of bacterial cell in this case. Thus, it was
concluded DNA replication proceeds through discontinuous mechanism.
2. Imagine a new DNA polymerase is discovered that can synthesise DNA in
the 3’ to 5’ direction. How would this change the mechanism of DNA
replication as we currently understand it?
If a DNA polymerase that copies DNA in the reverse direction (3’ to 5’) was
discovered, there would no longer be a leading or lagging strand or Okazaki
fragments. In the 5’ to 3’ direction, when DNA is replicated it only replicates in
this direction. Thus, there is the leading strand which synthesises continuously
in one large piece that starts at the replication fork. The other strand is
synthesised in fragments called Okazaki as the DNA polymerase cannot work in
the 3’ to 5’ direction. If a new polymerase was added that had this ability, the
leading and lagging strands are synthesised continuously.
, 3. Cellulose and starch are both polymers of glucose but fulfil very different
functions in cells. Explain the roles and properties of the two polymers.
Explain which of their properties may have aided the evolution of their
current function.
Starch is glucose’s energy storage form. Glucose units in starch are connected by
alpha linkages with glyscosidic 1-4 and 1-6 linkages. The branching structures
creates gaps between the bonded molecules. Due to these gaps, starch can be
broken down very easily (as they can access the gaps) and they have very simple
access to energy (which inturn, can then be broken down).
Cellulose is an aid for cell walls in plants. The glucose units in cellulose are
connected by beta linkages. They are comprised of 1-4 linkages, resulting in the
structure being linear. This makes the walls rigid and assists in maintaining the
wall’s structure. This also allows the molecules to pack tightly together, so the
bonds are harder to break. Thus, unlike starch, humans don’t have enzymes to
break down cellulose.
4. Describe the similarities and differences between glycosidic bonds (that
link individual sugars into polysaccharides) and peptide bonds (that form
between amino acids).
The key difference between glycosidic and peptide is the way they are formed.
Glyscosidic bonds are found in sugar molecules and peptide bonds are formed
between two amino acids. However the main similarties are that they are both
formed through dehydtration reactions and they both form polymers.
A glycosidic bond is a covalent bond between two monosaccharides (classes of
sugars that cannot be hydrolysed to give a simpler sugar and made of
polysaccharides). The link sugars to carbohydrate molecules (such as
polysaccharides) between two carbon atoms.
Glycosidic bonds are formed through dehydration reactions that unvolve
removal of water molecules in the process. However, the reverse reaction of
breaking a glycosidic bond is the hydrolysis reaction where one water molecule
is used. Forming the glycosidic bond occurs when the alcohol group (-OH) from
a monosacchride react with the anomeric carbon from a sugar molecule. The
anomeric carbon is the central carbon atom with single bonds to two oxygen
atoms. One oxygen atom is bonded to a sugar ring and the other is bonded to the
–OH group.
A peptide bond is an amide bond that links two alpha amino acids from carbon
number 1 and nitrogen number two along a protein chain. When the amino
group of an amino acid combines with the carboxyl group of another amino acid,
a peptide bond is formed. As a water molecule is removed in this process, it is
called a dehydration reaction.
5. Why do all cells need membranes? What are the chemical properties of
phospholipids that make them suited to this task?
1. How did Reiji Okazaki test if DNA replication was continuous or
discontinuous?
An Okazaki fragment is a short fragment of DNA (with RNA primer on 5’
terminus) which is created on the lagging strand throughout DNA replication.
This was discovered in 1968 by Reiji Okazaki and their colleagues during the
study of replication of bacteriophage DNA in E Coli.
Okazaki reasoned three possibilities for replicating double-stranded DNA. The
continuous model is impossible due to the nature of the polymerases (replication
in one direction). Thus, he needed to demonstrate semi-continuous or
discontinuous. For this, the pulse-labelling technique was used. Bacterial cells
infected with wild type/bacterial virus’ is given radioactively labelled DNA
precursor. With this, using sucrose, DNA molecules do not find their equilibrium
position, so molecules are always in motion. The ultracentrifuge must be stopped
at an experimentally determined time for the experiment to work. Here, DNA
synthesis has taken place during the pulse time producing radiolabeled thymine
located on the gradient.
During very short times of labelling, short pieces of DNA are found, With longer
times, pieces of DNA were increasing longer. Then he used the same experiement
with a defective mutant virus called DNA ligase. This is the enzyme joining
pieces of DNA together in larger structures. These labelled pieces of DNA
remained short, even after radiolabelling for long periods.
Further data suggested that DNA replication occurred by synthesis of small
pieces later linked together by DNA ligase. This was proved by a pulse-chase
experiment. His uninfected bacterial culture was radiolabeled for a short time,
which was followed by adding large excess of unlabelled precursor. The resulted
in a decrease in the quantity of radiolabel incorporated and allowed him to
follow fate of short pieces. The data then reflected that DNA which was labelled
during the 30 second pulse but eventually winds up in large DNA, which is
equivalent to the size of genome of bacterial cell in this case. Thus, it was
concluded DNA replication proceeds through discontinuous mechanism.
2. Imagine a new DNA polymerase is discovered that can synthesise DNA in
the 3’ to 5’ direction. How would this change the mechanism of DNA
replication as we currently understand it?
If a DNA polymerase that copies DNA in the reverse direction (3’ to 5’) was
discovered, there would no longer be a leading or lagging strand or Okazaki
fragments. In the 5’ to 3’ direction, when DNA is replicated it only replicates in
this direction. Thus, there is the leading strand which synthesises continuously
in one large piece that starts at the replication fork. The other strand is
synthesised in fragments called Okazaki as the DNA polymerase cannot work in
the 3’ to 5’ direction. If a new polymerase was added that had this ability, the
leading and lagging strands are synthesised continuously.
, 3. Cellulose and starch are both polymers of glucose but fulfil very different
functions in cells. Explain the roles and properties of the two polymers.
Explain which of their properties may have aided the evolution of their
current function.
Starch is glucose’s energy storage form. Glucose units in starch are connected by
alpha linkages with glyscosidic 1-4 and 1-6 linkages. The branching structures
creates gaps between the bonded molecules. Due to these gaps, starch can be
broken down very easily (as they can access the gaps) and they have very simple
access to energy (which inturn, can then be broken down).
Cellulose is an aid for cell walls in plants. The glucose units in cellulose are
connected by beta linkages. They are comprised of 1-4 linkages, resulting in the
structure being linear. This makes the walls rigid and assists in maintaining the
wall’s structure. This also allows the molecules to pack tightly together, so the
bonds are harder to break. Thus, unlike starch, humans don’t have enzymes to
break down cellulose.
4. Describe the similarities and differences between glycosidic bonds (that
link individual sugars into polysaccharides) and peptide bonds (that form
between amino acids).
The key difference between glycosidic and peptide is the way they are formed.
Glyscosidic bonds are found in sugar molecules and peptide bonds are formed
between two amino acids. However the main similarties are that they are both
formed through dehydtration reactions and they both form polymers.
A glycosidic bond is a covalent bond between two monosaccharides (classes of
sugars that cannot be hydrolysed to give a simpler sugar and made of
polysaccharides). The link sugars to carbohydrate molecules (such as
polysaccharides) between two carbon atoms.
Glycosidic bonds are formed through dehydration reactions that unvolve
removal of water molecules in the process. However, the reverse reaction of
breaking a glycosidic bond is the hydrolysis reaction where one water molecule
is used. Forming the glycosidic bond occurs when the alcohol group (-OH) from
a monosacchride react with the anomeric carbon from a sugar molecule. The
anomeric carbon is the central carbon atom with single bonds to two oxygen
atoms. One oxygen atom is bonded to a sugar ring and the other is bonded to the
–OH group.
A peptide bond is an amide bond that links two alpha amino acids from carbon
number 1 and nitrogen number two along a protein chain. When the amino
group of an amino acid combines with the carboxyl group of another amino acid,
a peptide bond is formed. As a water molecule is removed in this process, it is
called a dehydration reaction.
5. Why do all cells need membranes? What are the chemical properties of
phospholipids that make them suited to this task?
