DNA Structure

*Refer to this video if needed

Nucleic acids
● Nucleic acids (or polynucleotides) are the genetic material of all living things and
viruses, and are found in all organisms.
● They are macromolecules/polymers made by linking smaller monomers (i.e.
nucleotides) together.
● There are 2 types of nucleic acids: DNA (deoxyribonucleic acid) & RNA (ribonucleic
acid).
○ DNA is found in chromosomes, which are located within the nucleus.

Nucleotides (the monomers of nucleic acids)

● A nucleotide consists of a nitrogenous base, a pentose sugar, and phosphoric acid.
● The nitrogenous bases are derived from one of two parent compounds: purine or
pyrimidine.
○ Adenine (A) and guanine (G) are purine bases, while thymine (T)/uracil (U) and
cytosine (C) are pyrimidine bases.
● Differentiating between DNA and RNA:

● A nucleotide is formed through condensation reactions, resulting in the formation of two

water molecules.
Formation of a dinucleotide
A covalent bond (phosphodiester bond) is formed between the 5'-phosphate group of one
nucleotide and the 3'-OH (hydroxyl) group of another nucleotide. This bond is formed by a
condensation reaction and a water molecule is lost in the process.
Nucleotides become nucleic acids
● Nucleotides combine together to form nucleic acids (i.e.
polynucleotides) via condensation reactions between the
phosphate group of one molecule and the sugar of another.
● This creates a sugar-phosphate backbone, which is a
backbone of alternating sugar and phosphate molecules.
● Different bases are attached sideways along the strand. The
sequence of bases represents a unique genetic code.
DNA
● A DNA molecule consists of 2 polynucleotide strands held by hydrogen bonds
between paired bases, forming a double helix.
● Deoxyribose nucleotides, which are the monomers of DNA, contain nitrogenous bases
of cytosine, guanine, adenine, and thymine.
○ Pairing of bases (aka complementary base pairings) occur such that A=T and
CΞG, with two and three hydrogen bonds formed between them respectively.
○ Pairing of a purine to pyrimidine results in standard spacing between the
sugar-phosphate backbones, contributing to DNA stability.
● DNA strands are arranged antiparallel; one chain runs from 5' to 3' while the other runs
from 3' to 5'.
○ This allows for complementary base pairing between the 2 DNA strands, with
two hydrogen bonds formed between adenine and thymine and three hydrogen
bonds formed between cytosine and guanine.
● The role of DNA is to instruct cells to make specific polypeptides and proteins.
● In all organisms, the ratio of A:T and G:C is always close to 1, i.e. no. of G ≈ no. of C,
and no. of A ≈ no. of T.
○ This indicates that there is complementary base pairing between adenine and
thymine, as well as between cytosine and guanine.
RNA
● Contains ribose sugar (also a
pentose sugar) instead of
deoxyribose
● Relatively short in length, and is
single-stranded
● Contains uracil (U) instead of
thymine (T), i.e. adenine now
bonds to uracil instead of thymine
● 2 functional types: transfer RNA
(to be covered in unit 4) and
messenger RNA

Differences between DNA and RNA

DNA RNA

Length Very long strands, several million Relatively short strands

nucleotides long

Sugar Deoxyribose Ribose

Bases C, G, A and T (not U) C, G, A and U (not T)

Forms Consists of two polynucleotide Consists of single strands and exists in

strands in the form of a double helix two functional forms: messenger RNA
with complementary base pairs (C (mRNA) and transfer RNA (tRNA)
with G and A with T) held by
hydrogen bonds

Organisation of genetic material

● The role of DNA is to instruct cells to make specific polypeptides and proteins.
● Within the nucleus, DNA molecules are tightly packaged into thread-like structures
called chromosomes.
● Each chromosome is made up of DNA tightly coiled many times around histone
proteins.
○ Each chromosome contains one molecule of DNA. About 50% of a chromosome
is made of protein.
● A sequence of nucleotides makes up a gene (a section of DNA) and the sequence can
vary. This results in many different genes. Each gene controls the formation of a single
polypeptide, which determines a phenotype.
 DNA Replication
*Refer to this video if needed

DNA replication
● Must be an extremely accurate process since DNA carries the genetic message
● Takes place in the nucleus during interphase, before nuclear division.
● Strands of the DNA double helix are built up individually from free nucleotides.

Part 1: Separation of DNA strands

● DNA replication begins at the origin of replication (ori).
● Helicase unzips the double helix by breaking the hydrogen bonds between the
complementary base pairs in the parental strands.
● Each parental strand acts as the template for the synthesis of a new DNA strand.
● Note: DNA replication occurs from 5' to 3' (explained in the video linked above &
illustrated in the diagram below)

Part 2: Synthesis of RNA primer

● Primase attaches to the unwound chain and catalyses the synthesis of RNA primer to
provide free 3'OH ends for DNA Polymerase III.
Part 3: Synthesis of new daughter strand(s)
● DNA Polymerase III elongates the new daughter strands in 5' to 3' direction by
catalysing phosphodiester bond formation between the incoming
deoxyribonucleotides and free 3'OH end of the daughter strand.
● Free deoxyribonucleotides are incorporated by complementary base pairing to the
parental DNA strands, with adenine to thymine and guanine to cytosine.
● In a replication fork, the leading strand is synthesized continuously while the lagging
strand is synthesized discontinuously to form Okazaki fragments.
● RNA primers are removed and replaced by deoxyribonucleotides by DNA
Polymerase I.
● Nicks between the Okazaki fragments are filled in by DNA ligase by forming
phosphodiester bonds between Okazaki fragments.
The Meselson-Stahl experiment
 NOTE: the thickness of the bands matter!!

Describe and explain how the model of semiconservative DNA replication is supported
by the results from Generation 1 and 2.
Generation 1:
● Both the parental strands contain only heavy 15N. Each parental 15N-strand served as
the template for replicating a daughter 14N-strand, resulting in a hybrid DNA molecule
composed of one new daughter 14N-strand and one parental 15N-strand.
● Hence, in the first generation, the isolated DNA showed only one single band of
intermediate density, showing a hybrid DNA molecule.

Generation 2:
● Each of the hybrid DNA molecules now separate and serve as templates for replication.
The heavier 15N strands will form a hybrid DNA molecule with the 14N daughter DNA
strand, resulting in a band of intermediate density,
● while the other 14N parental strands will serve as a template for replicating a new
daughter strand, resulting in a daughter DNA molecule that is entirely 14N, resulting in a
higher/less dense band.

see ws1 (hardcopy) q10 for drawing of leading and lagging strands
 ● explanation for the positioning of numbers (5' written next to 3'): As new nucleotides are
added to a strand of DNA or RNA, the strand grows at its 3' end, with the 5′ phosphate
of an incoming nucleotide attaching to the hydroxyl group at the 3' end of the chain.

This is how the strands should be labelled: (from FA2)