Nucleic Acid:

Structure and function of DNA

(primary and secondary)

Lesson objectives:

§ Establish the connection between DNA structure and its function;

§ Describe the chemical structure of nucleotides and explain their bonding

and location in DNA molecules;
DNA (deoxyribonucleic acid) was firstly isolated by the Swiss physician Friedrich Miescher
in 1869.
Actually it was Rosalind Franklin’s discovery (X-ray diffraction picture of structure of
DNA) that led to Crick and Watson’s double helix model in 1953. She died from cancer at
the age of 37 in 1958.
Professor Maurice Wilkins received the Nobel Prize with Crick and Watson for three-
dimensional structure of DNA in 1962.

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One Strand of DNA
• The backbone of the phosphate
molecule is alternating
phosphates and
deoxyribose sugar
• The teeth are deoxyribose
nitrogenous bases.

bases

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 O
O -P O
Nucleotides
One deoxyribose together with
O
O its phosphate and base make a
O -P O nucleotide.
O O
O -P O
O Nitrogenous
O base
Phosphate
C

C
C

C C
O Deoxyribose
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One Strand of DNA
nucleotide
• One strand of DNA is a
polymer of nucleotides.
• One strand of DNA has
many millions of
nucleotides.

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Four nitrogenous bases
DNA has four different bases:
• Cytosine C
• Thymine T
• Adenine A
• Guanine G

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Two Kinds of Bases in DNA
N
• Pyrimidines are N C
single ring bases. O C C
N C

• Purines are double N

ring bases. N C
C C N
N C
N C

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 Thymine and Cytosine are pyrimidines
• Thymine and cytosine each have one ring of carbon and nitrogen atoms.

O
N
N C N C

O C C C
O C C

N C N C
thymine cytosine
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 Adenine and Guanine are purines

• Adenine and guanine each have two rings of carbon and nitrogen atoms.

N O

N C N C

C C N C C
N N

N C N C
Guanine C
Adenine
N C N

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Two Stranded DNA
• Remember, DNA has
two strands that fit
together something
like a zipper.
• The teeth are the
nitrogenous bases but
why do they stick
together?

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 Hydrogen Bonds
• The bases attract each other

N
because of hydrogen bonds.
• Hydrogen bonds are weak but

C
N

N
there are millions and millions
of them in a single molecule
of DNA.

C
C
O

N
• The bonds between cytosine
and guanine are shown here

C
with dotted lines N
C N

C C O

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C N
Hydrogen Bonds, cont.
O
• When making hydrogen N C
bonds, cytosine always
pairs up with guanine O C C C
• Adenine always pairs up N
with thymine N C
C
N
• Adenine is bonded to C N
thymine here
C
C C
N N

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Base Pairing

. . .

. . .

. . .

3 Hydrogen bonds

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 Base Pairing

. . .

. . .

2 Hydrogen bonds

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 The polymeric structure of DNA may be described in
terms of monomeric units of increasing complexity.

The three relatively simple components are.

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Bases attached to a sugar is called
nucleoside.
Sugar + phosphate + base =
nucleotide.
DNA only : Tymine, 2-deoxyribose

RNA only : Uracil, ribose

DNA and RNA : adenine, guanine,

cytosine
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deoxyribonucleotide

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deoxyribonucleotide

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deoxyribonucleotide

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deoxyribonucleotide

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 Types of bonds
in 2'-deoxycytidine-5'-diphosphate

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 Names of DNA Base Derivatives

Base Nucleoside 5'-Nucleotide

2'-Deoxyadenosine-5'-
Adenine 2'-Deoxyadenosine monophosphate
Adenylic acid
2'-Deoxycytidine-5'-
Cytosine 2'-Deoxycytidine monophosphate
Cytidylic acid
2'-Deoxyguanosine-5'-
Guanine 2'-Deoxyguanosine monophosphate
Guanidylic acid
2'-Deoxythymidine-5'-
monophosphate
Thymine 2'-Deoxythymidine
Thymidylic acid

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 25
3 end
 RNA are easily hydrolyzed under mild alkaline conditions to
nucleotides which is cleaved in alkaline medium the phosphoric
acid to form nucleosides, that are hydrolyzed in acidic medium to
the heterocyclic base and the sugar.

The secondary structure of DNA is determined by the spatial

organization of the polynucleotide chain.

The orientation of the heterocyclic base on each nucleotide

residue is perpendicular to the axis of the double helix.

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 According to the Watson-Crick model of a DNA molecule
consists of two polynucleotide chains forming a double helix
with diameter of 1.8 - 2.0 nm. At each turn of the helix are ten
base pairs.

The sugar– phosphate backbone runs along the outside of

the helix, and the amine bases hydrogen bond to one another on
the inside. Both major and minor grooves are visible.

Two polynucleotide strands are antiparallel to each other, so

direction of phosphodiester formation is opposite: one chain is 5'
- 3' end and the other of 3' – 5' end.
.

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DNA double helix fragment in space-filling and wire-frame
format

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 Chargaff principles:

•A always pairs with T in DNA.

•C also pairs with G in DNA.

•The amount of A is equal to the

amount of T, same for C and G.
•
•A+C = T+G
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Different levels of DNA structure to fit the enormously long DNA
duplexes into the nuclei of human cells.

highly supercoiled chromatin fiber

chromosome.

150 to 200 base pairs

two pairs
of 4 different
proteins

double helix DNA 31

Replication — the process by which identical copies of
DNA are made so that information can be preserved and
handed down to offspring.

Transcription — the process by which the genetic

messages are read and carried out of the cell nucleus to
ribosomes, where protein synthesis occurs.

Translation — the process by which the genetic messages

are decoded and used to synthesize proteins.

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Nicotinamide adenine
dinucleotide (NAD) is
one of the principal
oxidation-reduction
reagents in biological
systems.

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 Bial’s test
(pentose detection in products of nucleoprotein hydrolysis)

When reacted with concentrated solution of H2SO4 or

dilute HCl pentoses are dehydrated to form furfural
which is condensed with orcinol (3,5-dihydroxytoluene).

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 Bial’s test

Also they gave red products of condensation with

thymol (2-isopropyl-5-methylphenol).

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A mutation is an error in the base sequence of a gene.

The end result can be the alteration or cessation of a polypeptide’s or

protein’s functioning because of a change in its α-amino acid sequence.

There are two types of mutations:

• Substitution (point) mutations, in which one base substitutes for another in

the normal base sequence: one purine for another, one pyrimidine for
another, a purine for a pyrimidine, or a pyrimidine for a purine.

• Frameshift mutations, in which a base is inserted into the normal base

sequence or is deleted from it.

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 Antiviral drugs

DNA synthesis terminates whenever AZT is incorporated into the growing

DNA strands in the course of reverse transcription.
Protease inhibitors block step 7, the cutting up of the proteins produced by
the translation of viral RNA, by inactivating the enzyme protease.
New viruses are not produced.
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 Creating an information
scheme that should describe
the structure and function of
DNA

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 Compare your schema with
video info
• https://www.youtube.com/watch?v=o_-
6JXLYS-k

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Why do we study DNA?
We study DNA for many
reasons, e.g.,
• its central importance
to all life on Earth,
• medical benefits such
as cures for diseases,
• better food crops.

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Chromosomes and DNA

• Our genes are on our

chromosomes.
• Chromosomes are
made up of a
chemical called DNA.

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 The Shape of the Molecule

• DNA is a very long

polymer.
• The basic shape is like a
twisted ladder or zipper.
• This is called a double
helix.

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The Double Helix Molecule
• The DNA double
helix has two
strands twisted
together.

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Linear Polymerization of Nucleotides

• Nucleic acids are formed of

nucleotide polymers.
• Nucleotides polymerize
together by phospho-diester
bonds via condensation
reaction.
• The phospho-diester bond is
formed between:
• Hydroxyl (OH) group of the
sugar of one nucleotide.
• Phosphate group of other
nucleotide
Polymerization of Nucleotides
• The formed polynucleotide
chain is formed of:
• Negative (-ve) charged
Sugar-Phosphate backbone.
• Free 5’ phosphate on one
end (5’ end)
• Free 3’ hydroxyl on other
end (3’ end)
• Nitrogenous bases are not in
the backbone
• Attached to the backbone
• Free to pair with
nitrogenous bases of other
polynucleotide chain
Polymerization of Nucleotides
• Nucleic acids are polymers of nucleotides.
• The nucleotides formed of purine or
pyrimedine bases linked to phosphorylated
sugars (nucleotide back bone).
• The bases are linked to the pentose sugar to
form Nucleoside.
• The nucleotides contain one phosphate group
linked to the 5’ carbon of the nucleoside.
Nucleotide = Nucleoside + Phosphate group
DNA by the Numbers
• Each cell has about 2 m of
DNA.
• The average human has 75
trillion cells.
• The average human has
enough DNA to go from the
earth to the sun more than
400 times. The earth is 150 billion m
• DNA has a diameter of only or 93 million miles from
0.000000002 m. the sun.

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Almost all the cells in our body have DNA with the exception of
red blood cells.

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Summary of how DNA Structure is suited
to function:

• It is very stable: nucleotide are linked by covalent bonds.

• It Carries coded information.
• It can be replicated: specific base pairing means that DNA can
be copied when cells divide.
• It is compact: folding of the molecule means a great deal of
information can be packed into a small volume.

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 Fig. shows part of a DNA molecule.

(a) Name U, W and X.

U, W, X

(b) Name the bonds indicated by Z.

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Structure Link to function
Genes and chromosomes

DNA molecular structure (polymers)

the anti-parallel nature of the strands; the

asymmetric ends of DNA strands (the 5′
(five prime) and 3′ (three prime) ends, with
the 5' end having a terminal phosphate group
and the 3' end a terminal hydroxyl group);
Double helix and
complementary base pairing
Sequence of bases making up the genetic
code/Codon (covered in detail later);
the coding and non-coding strands

Packaging of DNA molecule-how and why?

(protection etc)

Histones
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Thank You for
Your
attention!