BIO LOGY

UNIT 02 MUF 0032

GUIDED GROUP LEARNING: DNA STRUCTURE AND REPLICATION

Manager: Maisa Reader: Lang Jian
Scribe: Lloaana Communicator: Leeroy

Introduction
Deoxyribonucleic acid, or DNA, contains the instructions for building all the structural and functional proteins
required by an organism. Every cell in a multicellular organism contains the complete set of DNA and therefore
the entire blueprint for the organism. As an organism grows or repairs damage, new cells are created. An exact
copy of the DNA is made before a new cell is formed.

How is the structure of DNA related to its ability to replicate without mistakes?
The bases between the 2 strands are complementary. Purine bases only join with the specific
complementary pyrimidine bases described with Chargaff’s rule/complementary base pairing (thyamine (T)
only pairs up with Adenine (A) and Guanine (G) only pairs up with Cytosine (C)). Therefore this reduces the
chance of an error occurring during replication.

Figure 1 – The structure of nucleotides and the models of DNA

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1. Refer to the nucleotide diagram in Figure 1.

a. Name the three components of a nucleotide.

Deoxyribose sugar , Nitrogenous Base , Phosphate Group

b. Identify the variable component (the part that can change) of a nucleotide.
Nitrogenous base

c. Name the sugar present in a DNA nucleotide.

Deoxyribose sugar

d. Identify the component of a nucleotide that contains the element nitrogen.

Nitrogenous base

e. The carbon atoms of the sugar are numbered in order from 1’ to 5’, starting at the carbon bonded to the
nitrogenous base. To which carbon is the phosphate group bonded?
5’ carbon group

f. When nucleotides bond together into chains, the OH group is removed to allow the phosphate group of
the next nucleotide to bond to the sugar. To which carbon does the new phosphate group bond?
3’ carbon group

2. Refer to the nitrogenous base diagrams in Figure 1.

a. Identify the structural difference between pyrimidines and purines.

Pyrimidines consist a single ring while purines consist of double ring.

b. Match the names of each nitrogenous base with their letter symbol.
A with T , G with C

3. DNA is a 3D shape, but it is often drawn as a ladder to show its structure more clearly. Locate this diagram in
Figure 1.

a. Circle one complete nucleotide on each side of the ladder model.

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 b. Which part(s) of the nucleotides make up the sides or ‘backbone’ of the DNA ladder?
Sugar – phosphate group

c. Which part(s) of the nucleotides make up the ‘rungs’ or cross pieces of the DNA ladder?
Nitrogenous base

d. Add 5’ and 3’ to the appropriate ends of each backbone in the ladder model diagram.

e. Do the two backbones, or strands, of the ladder model match (parallel) or do they run in opposite
directions (antiparallel)?
Antiparallel

4. a. Locate one nucleotide with a cytosine nitrogen base. Identify the nitrogen base it is bonded to on the
other strand. Does cytosine always pair with this nitrogen base? Write a base-pairing rule for DNA that
includes all four nitrogenous bases.
Guanine. Yes Cytosine always pairs with Guanine. By Chargaff’s rule, Adenine always pairs with Thymine
and Cytosine always pairs with Guanine.  
 

b. Pyrimidines and purines are different shapes. Explain how this affects the base-pairing rule you wrote in
part 4a.
Purines are made up of 2 rings while pyrimidines are only made up of a single ring. As seen from the base
pairing rule in the earlier part (Chargaff’s rule), in both complementary base pairs, it is always a purine
bonded to a pyrimidine. This ensures that each bonded base pair always has a total of 3 rings to allow for
even spacing between two sugar-phosphate backbones.  

c. The two strands of DNA are held together by hydrogen bonds between nitrogen bases. Hydrogen bonds
are relatively weak bonds between polar molecules. On the ladder model diagram, draw an arrow
pointing to a hydrogen bond and label it.

d. Some of the bonds between nucleotides are double hydrogen bonds and some are triple bonds. Rewrite
your base-pairing rule from part 4a and modify to include reference to hydrogen bonds.
The complementary base pair of Adenine and Thymine forms a double hydrogen bond while the
complementary base pair of Guanine and Cytosine forms a triple hydrogen bond.  
 

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Erwin Chargaff (1905–2002) investigated the ratio of nucleotide bases in DNA samples from a range of different
organisms. His findings suggested that certain nucleotides always paired together; adenine with thymine and
cytosine with guanine. This complementary base-paring rule become known as Chargaff’s rule.

5. a. Using the complementary base-pairing rule, write the missing nitrogenous bases below the strand shown.
A T C C G A G C G T
T A G G C T C G C A

b. Different species have different amounts of each nucleotide. Using the base pair rules, complete the
following table to show the percentage of each type of base in four different organisms.
Organism % of Adenine % of Guanine % of Thymine % of Cytosine

Human 21 30 19 30

Salmon 21 29 21 29

Wheat 27 23 27 23

Yeast 31 19 31 19

Chargaff’s rule, the X-ray diffraction photographs of DNA molecules taken by Maurice Wilkins and Rosalind
Franklin, and other research into the structure of DNA was eventually put together by James Watson and Francis
Crick. The Watson and Crick model of DNA describes the molecule as a double helix.

6. Examine the double helix diagram in Figure 1 and describe the shape of the DNA molecule. Your description
should include reference to at least 3 key features.
The double helical structure of DNA looks like a twisted ladder. The structure is held by 2 sugar-phosphate
backbones on each strand of DNA. The 2 strands of DNA are held together by the hydrogen bonds between
complementary bases (Chargaff’s rule). The adjacent nucleotides in each strand are held together by strong
phosphodiester bonds. These bonds help the DNA molecule maintain its double helix structure.  

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7. Examine Figure 2. Number the steps below to show the order of the key processes involved in DNA
replication.
___6__ Complementary free nucleotides are attracted to unpaired nucleotides on the DNA strands.
___1__ Hydrogen bonds between nucleotides are broken.
__4___ Primase forms a short strand of RNA on the exposed DNA to indicate where replication should begin.
___7__ Hydrogen bonds form between complementary nucleotides.
___3__ Single-stranded binding proteins bind to the single strands of DNA.
___5__ The sliding clamp attaches DNA polymerase to the end of the primer.
___2__ The two strands of DNA separate.

8. a. What type of biological molecules are DNA helicase, RNA primase and DNA polymerase? Justify your
decision.
DNA helicase, RNA primase and DNA polymerase are enzyme which is functional protein-
based catalysts the tertiary and quaternary structures of proteins enable enzymes to have
specific 3D shapes that are compatible with their substrates.

DNA helicase, RNA primase and DNA polymerase are enzyme which is functional protein-based
catalysts the tertiary and quaternary structures of proteins enable enzymes to have specific 3D
shapes that are compatible with their substrates.

b. What is the role of DNA helicase in DNA replication?

DNA helicase which can unwinds the double helix and breaks the hydrogen bonds
between nitrogen bases, separating the two strands.

c. Draw an arrow on Figure 2 to show the direction in which DNA helicase is moving.

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 d. The area where the two strands of DNA are separate is called the replication fork. Add this label to Figure

e. What is the role of the single-stranded binding proteins?

Single-stranded binding proteins attaches each strand of DNA preventing reannelings.

9. The original strands of DNA, called the parental strands, remain the same. However new complementary
strands are built using free nucleotides.

a. This type of replication is called semi-conservative replication. Semi = half; conserve = keep. Explain why DNA
replication is called semiconservative.
DNA replication is called semiconservative because only one strand of the new double helix is
synthesised.

b. DNA molecules can be tens of thousands of base pairs long. Mistakes in DNA replication can lead to
mutations, which may or may not be harmful to the organism. Suggest how semi-conservative replication
helps prevent mutations during replication.
Because semiconservative replication has a DNA template that has been formed accurately, meaning
that half of the strands is already correct, the probability of having errors in the newly formed strand
is reduced, which helps prevent mutations during replication.

10.DNA polymerase ‘reads’ the single-stranded DNA from the 3’ to the 5’ end.
a. Draw an arrow on Figure 2 to show the direction in which DNA polymerase is moving.
b. The strand in which DNA is replicated continuously (non-stop) is called the leading strand. Add
this label to Figure 2.

The other strand of DNA cannot be replicated continuously, because DNA polymerase moves away from the
replication fork, still in the 3’ to 5’ direction. This strand is replicated is short chunks called Okazaki fragments. As
each fragment is completed, the sliding clamp moves the DNA polymerase to the next primer closest to the
replication fork.

11. a.The strand that is replicated discontinuously, in chunks, is called the lagging strand. Add this label to Figure
2.
b. Draw a labelled arrow on figure 2 to show the direction of replication on the lagging strand.

12. Once replication has been completed, the RNA primers are removed and replaced with DNA. DNA ligase then
‘glues’ all the sections together.

a. What type of biomolecule is DNA ligase?

Enzyme

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b. Which of the strands would require DNA ligase more often? Justify your decision.
The lagging strand. This is because it uses more primers than leading strand. DNA ligase will have
many portion to join.

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