Nucleic acids 2020

Biochemical properties of nucleic
acids. Matrix biosynthesis process
Year 2021
Mahira Amirova
Associate Professor
Biochemistry Department
Azerbaijan Medical University
Year 2021
In The Name of Allah, The Most Merciful, The Most
Compassionate

NUCLEIC ACIDS (NA). SINGLE-stranded
RNA and DOUBLE-stranded DNA

DNA and RNA transmit the genetic
information to the cell

PURINE and PYRIMIDINE nitrogenous
bases of DNA and RNA

Xanthine and hypoxanthine are also purines,
but they are not costituents of nucleic acids.
Uric acid is also a purine, but this waste
product is washed out with urine.
Orotic acid is a pyrimidine, that does not
present in NA, but is used as an anabolic drug.
In normal urine, there are xanthine and uric
acid, but there is no guanine!
After incomplete hydrolysis of NA, nucleosides are formed:
(deoxy) adenosine,
(deoxy) guanosine,
(deoxy) cytidine,
(deoxy) thymidine,
Uridine
Purine nucleosides
Pyrimidine nucleosides
Purines and
pyrimidines not
present in nucleic
acids

Instead of Uracil present in RNA , in
DNA occurs Thymine.
(in RNA)
(in DNA)
CH3
In DNA is absent uracil, in RNA there is no thymine.

Adenine and Guanine bind ribose at 9th nitrogen
atom, while Cytosine and Thymine – at 1st
nitrogen.
Point of ribose connection
9 9 1 1

RIBOSE and DEOXYRIBOSE
In order not to mix atoms of nitrogenous base with
atoms of carbohydrate ring, the latter are indicated by the sign ` (prime)
Piont of nitrogenous base connection

STRUCTURE OF NUCLEOTIDE MONO-,
DI-, TRIPHOSPHATE

Nucleotide dAMP = nucleoside
(adenosine)+phosphate
NUCLEOSIDE
ADENOSINE
With incomplete hydrolysis of nucleic acid,
nucleoside and phosphoric acid are formed.

With complete hydrolysis of nucleic acid (NA),
nitrogen base, monosaccharide pentose and
phosphoric acid are formed.

TYPES OF NUCLEOTIDES
 (d)AMP, (d)ADP, (d) ATP - (deoxy)-adenylic acid
 (d)GMP, (d)GDP, (d)GTP - (deoxy)-guanylic acid
 (d)CMP, (d)CDP, (d) CTP - (deoxy)-cytidylic acid
 (d)TMP, (d)TDP, (d) TTP - (deoxy)-thymidylic
acid
 UMP, UDP, UTP - uridilyc acid
Cyclic nucleotides as cAMP, cGTP are the secondary
messengers in hormonal signal transmission
to the cell.

The primary structure of the NA is the sequence of
mononucleotides in the polynucleotide chain.
In the synthesis of NA, nucleoside-5'-
triphosphates are used as the main material.
Therefore, the 5'-end of NA always remains in the
form of 5'-triphosphate. But at the 3’-end always
present a free OH-group.
The polynucleotide has 3 structural levels: primary,
secondary and tertiary.
The primary structure of DNA is determined by
spliting DNA with restrictase enzymes into small
fragments. Each restrictase is specific for a certain
nucleotide sequence.

The secondary structure of RNA is formed due to the
binding of nitrogenous bases in some sites according to the
principle of complementarity.
Types of RNA are: r-RNA, t-RNA, m-RNA.
ап
To the tertiary
structure

tRNA secondary structure (clover leaf)
Acceptor
arm
Region of hydrogen binding
between nitrogenous bases
Anticodon arm
Alkylated purine
Amino
acid
Extra arm

5.8S rRNA and 5S rRNA.
Structure is formed due to hydrogen binding between
nitrogenous bases
5.8S 5S

RIBOSOME OF E.coli.
rRNA is a framework for ribosome

Mononucleotides unite into polynucleotide via 3’, 5’-
phosphodiester bond
DNA
RNA may also have a 2’5’ bond.

Structure of Nucleic acids. DNA follows complementarity
rules

2 hydrogen bond are formed between A and T, 3
hydrogen bonds between G and C
Complementarity means:
binding of A with T only and
G –with C only.

The secondary structure of the NA is the spatial configuration of
the NA. For DNA, the Chargaff’s law are valid:
• 1. Sum of purines is equal to pyrimidines:
A + G = C + T.
• 2. The number of A will equal T,
and G = C.
• 3. А + C always equals G + Т
(for RNA this А + C= G + U rule is valid only).
• 4. G+C/ A+T. This is the DNA specificity ratio . In
human, the DNA is of the adenine-thymine type,
since its ratio equals 0.6.

Histones and protamines are connected with DNA.
These proteins are simple proteins of alkaline nature
present in cell nucleus. According to the modern
classification, they are not proteins, but peptides.
Examples of protamines from fish are:
•salmine from salmon
•Scumbrin from mackerel
•clupeine from herring
•iridine from rainbow trout
•thinnine from tunafish
•stelline from starry sturgeon
•scylliorhinine from dogfish

There are mono-, di- and tri-protamines.

HISTONES CONTAIN BASIC AMINO
ACIDS
• Histones contain a lot of arginine and lysine,
so their pİ = 9-12.
In histones, tryptophan does not occur.
• In the nucleosome, the DNA helix is wrapped
1.75 times around 8 histone molecules.

HISTONES PROVIDE CONDENSATION OF chromosome and DNA turning. In chromatin
present DNA, histones, non-histone proteins (regulate chromatin’s activity), some RNA.
In the nucleus of each cell, the DNA molecule is packaged into thread-
like structures called chromosomes. Ergo, eukaryotic DNA is found in the chromosome of
the nucleus. DNA is also found in mitochondria.

TYPES OF HISTONES
The DNA region between the nucleosomes
is associated with H1 histone.

Euchromatin and heterochromatin
IS MORE ACTIVE
Compact, NOT VERY
ACTIVE

• REPRODUCTION by DNA (RNA) its own
ANALOGUE IS REPLICATION.
IT PROCEEDS ON THE BASIS OF
COMPLEMENTARITY.
GENETIC INFORMATION IS TRANSMITTED BY THE
MECHANISM OF THE MATRIX.
• THE TEMPLATE for replication and transcription
can be DNA OR RNA.
According to Watson and Crick model, REPLICATION
FOLLOWS SEMI-CONSERVATIVE PATH

DNA-TOPOISOMERASE CHANGES THE NUMBER
OF TURNS IN DNA HELIX. IT WEAKENS OR
STRENGTHENS DNA STRUCTURE (At initiation of
replication DNA topoisomerase breaks 3'5’-
phosphodiester bonds in DNA. When replication ends,
the same enzyme stitches the break point).
HELİCASE, at the expense of ATP uncoils double
HELIX of DNA.
DNA polymerase synthesizes DNA.
ONE POLYMERASE IS PRIMASE, SYNTHESIZING
OLIGORIBONUCLEOTIDE. First the primer, oligo-RN is
synthesized.

HELICASE, TOPO-ISOMERASE (breaks and stitches
3’5’phosphodiester bonds), LIGASE, PRIMASE,
POLYMERASE
HELICASE uncoils
double helix
TOPOISOMERASE
changes the number of turns

Therefore the
5’END (as in all
triphosphates) is
aways in the form
of TRIPHOSPHATE
While 3’END has a free OH-
GROUP
In the synthesis
oF NA as the
primary matherial
are used NTPs
(nucleoside
triphosphates)
DNA replication proceeds in 3 steps:
1) Initiation;
2) Elongation;
3) Termination
3`-End
5`-End

The lead chain is synthesized in the direction of DNA
unwinding, i.e. 5’ ⟹ 3 ’. Therefore, the lead chain is
synthesized faster.
The lagging chain is synthesized more slowly, because it is synthesized in the direction opposite
to unwinding, in the form of Okazaki fragments. About 200 mononucleotides present in each
Okazaki fragment.
For each Okazaki fragment a
primer, a short oligo-
ribonucleotide, is also
synthesized. This synthesis also
occurs in the direction 5’3 ’

TERMINATION of replication: REPLICATION STOPS
AFTER THE FORMATION OF COMPLETE
COMPLEMENTARY COPY OF DNA

TRANSCRIPTION is the SYNTHESIS OF
RNA ON DNA.
The transcriptional template can be DNA and RNA.
RNA SYNTHESIS IS PRODUCED BY RNA-POLYMERASE,
or TRANCRIPTASE.
 First are formed immature pre-rRNA, pre-mRNA and
pre-tRNA.
RNA-POLYMERASE I SYNTHESIZES rRNA
RNA-POLYMERASE II SYNTHESIZES mRNA
RNA-POLYMERASE III SYNTHESIZES tRNA
When DNA IS SYNTHESIZED ON RNA, IT IS A REVERSE
TRANSCRIPTION

Transcribed DNA is located in the fragment between
the nucleosomes, or on the linear nucleosome.
Globular
nucleosome of DNA
is always inactive.
Linear nucleosome

The TRANSCRIBED REGION OF DNA (between promoter
and terminator) is called TRANSCRIPTON (operon)
3` cystrons (informative section of transcripton) 5`
cistron
Informative part of cistron is called EXON.
terminato
pre-
ewly synthetized polypeptide,
on-active
(processing)
(active)

(Informative part of transcripton)
(Transcripton)
Start points

There is a PROMOTER on the top of transcripton.
PROMOTER site is called an operator in prokaryotes.
This site binds RNA-polymerase
•
Cistrone is a structural DNA gene, which stores information about
RNA that is responsible for amino acid sequence in protein.
There is a terminator site at the end of operon . It stores an
information about the end of transcription.
Promoter site,
binds RNA-
polymerase
Terminator site

ADDITIONAL REGULATORY SITES of
operon
Acceptor (regulatory) zone follows promotor
site. It is sensitive to regulatory factors. It
binds the repressors and can stop
transcription if needed.
Enhancer zone is an inductor zone, which
enhances transcription rate if needed.

Transcription proceeds in 3 steps:
INITIATION
ELONGATION
TERMINATION

RNA-polymerase. There are α-, β-, δ-
RNA-polymerases.
• As all polymerases, RNA-polymerase moves in
direction 5’3’, i.e. in direction of unwinding.
• As always, 3’-end comprises free OH-, while
5’-end ends with triphosphate.
The synthesis of all RNA starts with purines
(Adenine or Guanine)

POST-TRANSCRIPTIONAL PROCESSING
OF RNA
4 CHANGES in pre-RNA:
1) -CLEAVAGE OF non-informative introns
2) -SPLICING OF exons by ligases
3) -POLYADENYLATION of 3’end
4) -KEPING of 5’end, that increases the resistance of
RNA to nucleases. In kep, 5’5’ phosphodiester bond
is formed with the methyl-GTP

For a protein-coding gene, the RNA
copy, or transcript, carries the
information needed to build a
polypeptide (protein).
poly-Adenyl site
C
A
P
EXONS

In the end, we obtain a
MATURE mRNA
-OH
MATURE RNA is transferred from nucleus to cytoplasm with protein INFORMER.

Reverse transcriptase of oncoviruses,
tumor cells
1. Reverse transcriptase (RNA –DEPENDENT DNA-
polymerase) SYNTHESIZES DNA on RNA
template.
2. There is also RNA-REPLICASE, THAT SYNTHESIZES
RNA on RNA.
• Mutation mean any change in the DNA. We can
refine that definition: a mutation is a change in
the DNA base sequence, that results in a change
of amino acids in the polypeptide coded for by
that gene.

Spontaneous DNA damages are:
1) replication errors
2) depurination
3) deamination, when adenine becoms hypoxanthine, guanine -
xanthine, cytosine - uracil.
Physical and chemical factors result in following damage effect:
1. Alkylation of nitrogenous bases. During this process, the
formation of methyl guanine, methyl adenine occur.
2. Dimerization of pyrimidines under the UV radiation. Two
neighboring pyrimidine form a dimer called thymine dimers.

Reparative enzymes change the “mistaken” nucleotides to
the “healthy” ones.Their insufficiency leads to severe diseases,
for example xeroderma pigmentosum. Violation of reparative
system breaks renovation of damaged DNA. Reparative, anti-
mutagenic enzyme system includes:
• DNA exonuclease, which cleaves the damaged area.
• Uracil-DNA-glucosidase, which cleaves uracile from
deoxyribose.
• β- DNA polymerase and DNA ligase.
Reparative enzymes

XERODERMA PIGMENTOSUM- disease based on
insufficiency of DNA reparative enzymes
These patients do not
have DNA-nucleases to
break off the error
nitrogenous bases.
Severe sunburn after only a
few minutes in the
sun, freckling in sun exposed
areas, dry skin, changes in
skin pigmentation are only
few symptomes of this
disease.
Its severe form is called
De Sanctis-Kakkone.

RNA types
rRNA makes up more than 80% of cell RNAs (more
than any other RNA), has the largest molecular weight and
accumulates in the ribosome. It works as a framework of
ribosome.
mRNA is a template for reading the sequence of
amino acids in the peptide chain

One triplet encodes one amino acid
Initation triplet
mRNA

: mRNA
D
N
A
m-RNA constitutes minimum amount of cell RNAs, 5% only.
mRNA is synthesized on DNA cistron according to the principle of
complementarity. The mRNA consists of the codon triplets. Each
triplet encodes certain amino acid.
The genetic code consists of 61 «amino-acid coding codons» and
three termination codons, which stop the process of translation.

tRNA features
tRNA is abundant in minor nucleotides. Minor pyrimidines are:
methyl-cytosine, hydroxymethyl-cytosine, methyl uracil,
thio-uracil,
dihydro-uracil.
Minor nucleoside is:
pseudouridine
tRNA is called soluble RNA. It transports amino
acids to the ribosome. Each t-RNA can bind only
one amino acid. Ergo, there are at least 20 tRNAs.

MINOR pyrimidine of tRNA, methyl-cytosine
cytosine Additional methyl group
in methyl-cytosine

SECONDARY structure of tRNA resembles to a
“clover leaf”.
CCA-
end
on the complementarity
principle
Reading direction
The amino
acid is
attached to
3’end
adenine -OH
group.
Consequently
, the CCA
triplet on
tRNA 3’end
is called the
“acceptor
zone”.
At the 5’-end occurs G.
3’-terminus ends with a
C-C-A triplet. Ergo, 3’-terminus of
tRNA always ends with A

TERTIARY structure of tRNA
The tertiary structure of
tRNA resembles to an elbow
bend. This structure is
formed by van der Waals
forces.
Elbow bend
tRNA has 4 loops. The most
important of them is the
anticodon. Anticodon, a three
nucleotide containing triplet,
determines the type of tRNA.
This triplet corresponds to the
mRNA codon on the principle
of complementarity.

TRANSLATİON – synthesis of protein
template

Cell produces protein.
Transcription, translation
tRNA brings the
amino acid to the
ribosome, a place of
protein synthesis

Degradation of RNA depends of cell
needs.
If protein production is low, mRNA is
degraded more

PROTEIN SYNTHESIS PROCEEDS IN 4
STEPS
I. TRANSCRIPTION
II. Amino acid activation and recognition
III. TRANSLATION. It is a transfer of the
information from RNA to the structure of on
polypeptide chain of PROTEIN.
GENETIC INFORMATION IS TRANSMITTED by the
mechanism of the MATRIX.
IV. Post-translational processing

STAGES OF TRANSLATION
Translation comprises of 3 stages:
A) initiation, B) elongation, C) Termination.
Elongation proceeds from the N-end to the C-end in 3 stages :
1) Recognition of the codon. This stage ends with the connection of
aminoacyl tRNA with mRNA.
2) At Trans-peptidation, when a peptide bond is formed.
3) Translocation. It occurs when mRNA moves 1 triplet on the
ribosome to 3` end.

tRNA brings amino acids to A-center of ribosome. Formyl-
methionine is the first amino acid of synthesized peptide. It
enters P-center

CODONS ARE UNIVERSAL, i.e. they act
in all living organisms
 In ribosome, Amino acyl (A), Peptidyl (P)
centers and Exit zone occur.
 Synthesis starts with GUG or AUG triplet.
So, they are initiating codons.
 The initiation codon is the codon of N-
terminal methionine (in procaryots – formyl-
methionine).

INITIATION: formyl-methionine enters
P-center
The mRNA program is always read from the 5'end to the 3'end.

ELONGATION PROCEEDS IN 3 STAGES FROM N-END TO
C-END. There are three positions for tRNA in ribosome
Aminoacyl center called A-center, which is the binding site of an aminoacyl-tRNA with a
ribosome.

Amino acid is activated in 2 stages:
1st stage:
Mg2+
amino acid + АТP aminoacyl adenylate
2nd stage:
the formation of
aminoacyl-tRNA, i.e.
binding of amino acid to 3 ’-
OH end of tRNA.

tRNA binded to amino acid. Recognition of the codon leads to
the connection of aminoacyl tRNA with mRNA.

Terminal 3`OH-group of adenosine in
CCA triplet in accepting arm
tRNA CCA
(acceptor) end.
Adenine binds
amino acid
through 3`-OH
group

2) TRANSPEPTIDATION -formation OF
PEPTIDE BOND
Each peptide bond is formed at the expense of 4 high energy bonds (2ATP, 2GTP).
Despite the fact that the peptide bond contains only 21 kJ of energy, 140 kJ of energy is
expended on its formation.

3rd stage of translation, Translocation occurs when mRNA
moves 1 triplet on the ribosome to 3` end.
1) peptidyl-tRNA moved from the A-zone of ribosome to the P-
zone.
2) mRNA moves 1 codon on the ribosome in direction to 3`end,
3) tRNA leaves P-zone, then E-zone
E
A
P

3) TRANSLOCATION in Translation- mRNA moves 1
triplet.
 mRNA shifts 1 codon in 5`, 3` direction,
 tRNA leaves P-site to leave the ribosome through Exit zone,
 peptidyl-tRNA moves from A-zone to P-zone
with `Met
empty
2nd amino acid
GENERAL DIRECTION OF SYNTHESIS: 5` 3`
1st 2nd 3rd amino acid
4th amino acid

WHEN A TERMINATION codon includes into the A-SITE
of the ribosome, the RELEASING FACTOR BINDS TO THis
SITE and STOPS TRANSLATION
• TERMINATION is encoded by
UAA, UGA, UAG codons.
• Upon termination, the releasing factor binds
to the ribosome, after which ribosomal
complex and mRNA are separated.
FOR EACH PEPTIDE BOND WE SPEND 140KJ OF
ENERGY.

UAA encodes termination: thanks to p-protein,
ribosomal particles and protein are separated
When a termination codon (UAA, UGA, UAG. ) enters into the A site ,
a releasing factor (p-protein) binds to the site, stops the translation
and provides the releasing of the ribosomal complex and mRNA.

POST-TRANSLATIONAL MODIFICATION
(PROCESSING)
1)DEFORMYLASE cleaves formyl from formyl-methionine.
2)The N-terminal amino acid is acetylated.
3) Addition of glycosyl-, phosphate-, carboxyl-, hydroxyl-,
groups, iodine etc. occurs. Between cysteine molecules, disulphide
bond is made.
- Carbohydrates (glycosyl groups)are associated with serine,
threonine, asparagine.
- Phosphate binds to serine and threonine.
- 𝐴𝑑𝑑𝑖𝑡𝑖𝑜𝑛𝑎𝑙 carboxyl group binds with glutamic or aspartic
acids.
- Lysine and proline are hydroxylated.
4) The prostetic group is associated with its apo-protein part.
5) Partial proteolysis converts proinsulin to insulin, pro-
parathormone – to parathormone

REGULATION OF SYNTHESIS
CONSTITUTIVE PROTEINS are constantly synthesized in
the cell (for them, inductor is not needed)
INDUCTIVE PROTEINS NEED AN INDUCTOR FOR THEIR
SYNTHESIS. These proteis depend on the condition of
the life.
 Anabolic drugs enhance the synthesis of proteins.
Hypoxantine –riboside, potassium orotate are non-
hormonal anabolics.
 Antibiotics inhibit the synthesis of proteins

Nucleic acids 2020

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