BIOLOGY

DNA and DNA REPLICATION

Notes
DNA as the genetic material of all living organisms

● GENETIC MATERIAL or hereditary information (as its inherited) → store of

information
➔ If copied it can be passed :
➢ From cell to cell
➢ From parent to offspring
● NUCLEIC ACIDS :
➔ Very large molecules
➔ Made from nucleotides (the monomers/ subunits)
➢ Link to form a polymer
➔ 2 types of nucleic acids :
➢ RNA → ribonucleic acid
➢ DNA → deoxyribonucleic acid
● VIRUSES → some viruses have genetic material but they are not considered alive as
they don’t reproduce on their own but instead they rely on host cells. (Reproduction
is a fundamental property of living organisms).

Components of a nucleotide

NUCLEOTIDE → Pentose sugar + phosphate group + nitrogenous base

 ● Pentose sugar → a sugar with 5 carbon atoms
➔ Carbon atoms are numbered : from C1 to C5

● Phosphate group → acid and negatively charged part of nucleic acids

● Nitrogenous base → contains nitrogen and has either 1 or 2 rings of atoms in its
structure.

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Bases in each nucleic acid that form the basis of a code

● 4 different bases in DNA and RNA.

● All of the bases contain nitrogen → nitrogenous bases
● Any 2 nucleotides can be linked together because the phosphate group and sugar
used to make the bond are the same.
● Nitrogenous bases bond together through hydrogen bonding :
➔ Cytosine always pairs with Guanine
➢ 3 hydrogen bonds between each other
➔ Adenine always pairs with Thymine in DNA and with Uracil in RNA
➢ 2 hydrogen bonds between each other
● In bases :
➔ 1 ring of carbon atoms = pyrimidines
➔ 2 rings of carbon atoms = purines

DNA RNA

Adenine (A) Adenine (A)

Cytosine (C) Cytosine (C)

Guanine (G) Guanine (G)

Thymine (T) Uracil (U)

SEQUENCE OF BASES → how information is stored

● Stored in a coded form = universal genetic code shared by all organisms

Sugar-phosphate bonding and sugar-phosphate

“backbone” of DNA and RNA

● COVALENT BONDS → formed between the phosphate of one nucleotide and the
pentose sugar of the next nucleotide to join nucleotides together to form a polymer.
➔ Nucleotides are always added by adding nucleotides on the sugar end,
creating a series of alternating sugar and phosphate groups.

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 ➔ Covalent bonds between carbon, oxygen and phosphorus atoms form a
strong sugar-phosphate backbone in DNA and RNA molecules.
➢ Helps to conserve the sequence of bases

DNA as double helix of antiparallel strands of nucleotides

● DNA is composed of strands/ polymers of nucleotides.

➔ Phosphate group - pentose sugar - base }- linked by covalent bonds
➔ Sugar is deoxyribose
➔ COMPLEMENTARY BASE PAIRING AND BONDS =
➢ Adenine (2 hydrogen bonds) Thymine
➢ Cytosine (3 hydrogen bonds) Guanine
● Strands are antiparallel to each other in order to allow bases to pair
● Helical shape → constant diameter of 2nm

Condensation reaction
Nucleotides join together through condensation reaction (reverse is hydration reaction as
the product of the condensation reaction is H2O) → phosphodiester bond formed

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 ● It is an anabolic reaction → requires energy, as is bond forming → endothermic
reaction
➔ Opposite is catabolic reaction → does not require energy (bond breaking e.g.
digestion) → exothermic reaction.

Differences between DNA and RNA

DNA RNA

Number of strands 2 1

Bases Adenine, Guanine, Thymine, Adenine, Guanine, URACIL,

Cytosine Cytosine

Sugar Deoxyribose (H) Ribose (OH)

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DNA other

Role of complementary base pairing in allowing genetic

information to be replicated and expressed
● Allows an exact copy of DNA molecule to be made in a process called replication
● This means that te newly synthesized strand on each of the two templates has the
same base sequence as the other template strand.
● Replication is semi-conservative as when 1 DNA molecule is replicated, both 2 DNA
molecules that result have 1 new strand and 1 original strand.
● Genetic information → sections of DNA called genes, if it has an effect on the cell is
called gene expression.

Diversity of possible base sequences and limitless capacity of DNA for storing
information

With n bases there ae 4n possible sequences (essentially limitless)

Diameter of DNA molecule is 2nm → immense lengths of DNA can be stored in very small
volume (economical in terms of space and amount of material used to make it)

Conservation of genetic code across all life forms as

evidence of universal common ancestry
● Groups of 3 bases = codons
● 64 different codons
● 4x4x4 combinations
● Most codons specify one particular amino acid
● One codon (AUG) signals that protein synthesis should start and codes for an amino
acid as well : methionine
● 3 codons are stop codons - signal that protein synthesis should stop
● All lying organisms and viruses use same genetic code → universal
● Only very little differences in specific cases, mostly one stop codon instead codes for
an amino acid.

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Directionality of RNA and DNA
● Pentose sugar of the nucleotide at one end of the strand is unlinked → 3’ terminal
because C3 (carbon atom number 3) in this sugar is available for linkage to another
nucleotide
● The phosphate group of the nucleotide at the other end of the strand is unlinked →
5’ terminal because within a nucleotide, the phosphate group is attached to the C5
of the pentose sugar.

Purine to pyrimidine bonding as a component of DNA

helix stability
The nitrogenous bases in DNA are in two chemical groups :

● Purine → two rings of atoms : adenine and guanine

● Pyrimidine → 1 ring of atoms : cytosine and thymine

Each pair in DNA has 1 purine and 1 pyrimidine → 2 base pairs are of equal width and
require the same distance between the two sugar-phosphate backbones in double helix =
helps to make structure of DNA more stable and allows any sequence of bases in genes on
a DNA molecule.

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Chargaff’s data on the relative amounts of pyrimidine and purine bases
across diverse life forms

BEfore structure of DNA was known, scientists hypothized that it would contain a repeating
sequence of 4 bases = 4 nucleotides occurred in equal numbers

To test the tetranucleotide hypothesis Erwin Chargaff et al analyzed DNA samples from
range of species to find their nucleotide composition.

Structure of a nucleosome
● At core of nucleosome = 8 histone proteins.
● 2 copies each of 4 different types of histone together make up a disc-shaped
structure
● DNA is wound approximately twice around this protein core.
● An additional histone protein H1 reinforces the binding of the DNA to the
nucleosome core and helps in the packaging of chromosomes when nucleus is
preparing to divide.
● There is a short section of linker DNA between adjacent nucleosomes

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Evidence from the Hershey-Chase experiment for DNA as
the genetic material
● In early 1900s it was not clear wich molecules was the genetic material.
● Until the 1940s most biologists believed that protein was the most likely candidate
as it contains 20 types of amino acids whereas DNA only has 4 nucloetides
● To investigate this, Alfred Hershey and Martha Chase chose to use T2 bacteriophage
to identify the genetic material.
● In 1950s it was known that virus can transform a host cell so that it produces viral
proteins and for this to happen, viral genes must be injected nin host cell.
● Took advantage of the fact that DNA contains Phosphorus but not sulfur and that
proteins contain sulfur but not phosphorus.
● They cultured some viruses that contained proteins radioactively labelled through
label of 35S and other viruses that contained lable of radioactively labbelled 32P.
● Infected separate groups of bacteria with 2 viruses
● For each group they used a blender to separate non-genetic component of the virs
and they they centrifuged the culture solution to concentrate the cells in a pellet
● The cells were expected to contain radioactive genetic component of the virus.

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 ● Radioactivity was measured in pellet and supernatant
● Higher phosphorus radioactivity in pellet compared to supernatant and other way
around for sulfur = DNA is genetic material

DNA REPLICATION

DNA replication as product of exact copies of DNA with

identical bases sequences
● Replica = exact copy o something
● DNA REPLICATION → production of new strands of DNA with base sequences
identical to existing strands

DNA replication is required for :

● Reproduction → offsprings need copies of base sequences of their parents

therefore parents replicate their DNA to reproduce
● Growth and tissue replacement in multicellular organisms → each cell needs the
genetic material and therefore before a cell divides into 2 daughter cells, it must
replicate all of its DNA.

Steps of replication summary

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Semi conservative nature of DNA replication and role of
complementary base pairing
● When DNA is replicated, two strands must separate
● Both original strands are used as templates to guide the polymerization of a new
strand.
● REPLICATION FORK → the site at which the copying is actively occurring
● Once replication is complete, there are 2 DNA molecules both composed of an
original strand and a newly synthesized strand = replication is referred to as
semi-conservative.
● Base sequences on template strands determine bases sequences on the new
strand.
➢ Because complementary bases form hydrogen bonds with each other
stabilizing the structure
● Complementary base paring →
➢ Ensures that two DNA molecules resulting from DNA replication are identical
to the parent molecule
➢ Ensures high degree of accuracy when new strands are assembled on a
template strand
● 1 in 10 billion bases is incorrect when DNA is replicated
● Diploid human cell → 6 billion base pair = 0.6 errors when DNA is replicated.

Role of helicase, DNA polymerases, ligase and primase in

DNA replication
● DNA replication is a multi stage process that is carried by an assemblage of
functional subunits called REPLISOME
➢ Helicase and DNA polymerases (III and I) are two types of protein that are
essential parts of replisomes as well as DNA primase and DNA ligase

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Helicase

● Helicase is a ring shaped protein that separates the two strands of DNA molecule so
that each act as a template for the formation of a new strand
● As it moves along the molecule helicase breaks hydrogen bonds between bases,
allowing one strand to be pulled through the hole of helicase’s ring and the other to
pass aside it. → causes DNA double helix to uncoil

Unwind and Unzipping DNA

The unwinding of DNA double helix and unzipping (separation of 2 strands) causes tension
which is relieved by parts of the replisome, mainly DNA topoisomerase .

DNA topoisomerase

Releases tension caused by uncoiling and unzipping of DNA by Helicase

DNA primase

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 ● Type of RNA polymerase that assembles during replication a chain of about 10
ribonucleotides on the template strand.
● Chain of ribonucleotides added = primer and it provides a site were DNA
Polymerase III can bind and start adding nucleotides to 3’ end
● On leading strand : RNA primer is only added once
● On lagging strand : RNA primers inserted every 100-200 nucleotides as the
replication goes in the opposite direction to fork movement.

DNA polymerases

● Assembles new strands of DNA using 2 original strands as templates.

● Replisome contains separate DNA polymerases for each strand
● DNA polymerase brings nucleotides into the position where hydrogen bonds could
form.
● Links nucleotides end to end of the new strand by making covalent bonds between
phosphate group of free nucleotide and the sugar of the nucleotide at the end of
the new strand → phospho diester bonds.

DIRECTIONALITY OF DNA polymerases

● 3’ the end that terminates with the sugar → site available for a link to another
nucleotide is the third carbon of the sugar of terminal nucleotide
● 5’ end = phosphate group that is linked to 5th carbon atom on sugar
● Directionality of DNA polymerase is always 5’ to 3’ as 5’ phosphate of a free
nucleotide is linked to the 3’ end of growing strand

DNA Polymerase III DNA Polymerase I

● Principal polymerase in DNA ● Is both an exonuclease and a

replication polymerase as it can both break and
● Binds to template strand on 3’ side make hydrogen bonds between
of RNA primer nucleotides
● Assembles a chin of nucleotides in a ● On lagging strand, DNA polymerase
5’ to 3’ direction (phosphodiester I binds to the junction between the
bonds as well) 3’ end of an Okazaki fragment and
● Continues until end of template the 5’ start of an RNA primer. It
strand or another RNA primer is moves along the primer, removing
reached the RNA nucleotides and replacing

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 ● Proofreads each nucleotide after it them with DNA nucleotides.
has been added to the chain and ● It detached when reaches next
corrects mistakes by removing wring Okazaki fragment.
nucleotide and recruiting correct
one

DNA PROOFREADING

● DNA polymerases replicate DNA with great fidelity and where errors are made, they
are usually corrected, preventing mutations.
● There are multiple methods to prevent mutations, the earliest one is ‘proofreading’
and it happens during replication immediately after a nucleotide with mismatched
base has been added.
● In prokaryotes proofreading is done by DNA polymerase III as described above

DNA ligase

● Connects the gaps in the chain nucleotides left by DNA polymerase I by making a
sugar-phosphate bond : phosphodiester bond between Okazaki fragments

Differences between replication on leading strand and the

lagging strand
DNA can only assemble new strands in a 5’ to 3’ ndirection. Strands formed when helicase
separates the DNA are antiparallel (5’ to 3’ directions are opposite).

● On leading strand , DNA polymerase adds nucleotides moving towards the

replication fork = replication is continuous → completed more quickly
● On lagging strand, DNA polymerase adds nucleotides move away from the
replication fork.
➢ Must be added in a series of lengths as replication fore exposes more of the
template strands
➢ Short lengths of new DNA = Okazaki fragments
➢ Having to restart replication by DNA polymerase repeatedly makes the
process relatively slow.

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