Material Review of Nucleic Acid

By: Irvandar Nurviandy | 16030194039 | PKU 2016

Lecturer: Prof. Dr. Leny Yuanita, M.Kes.

Ribose and deoxyribose are types of monosaccharides (carbohydrates). What distinguishes

ribose and deoxyribose lies in C number 2, where in ribose C number 2 is bound to OH-group
while in deoxyribose is bound to group H

D-ribose or D-deoxyribose which binds to the pyrididine base will form nucleosides.
Nucleosides that bind to phosphate groups will form nucleotides. A collection of several
binding nucleotides is called nucleic acid. Nucleic acids that bind to proteins are called
nucleoproteins. Where cells consist of many nucleoproteins. There is 2 types of nucleoprotein:
• DNA nucleic acid
• RNA nucleic acid
Purin Base
The main one is nucleotides: adenine, guanine.
On tRNA: hypoxanthine, 1-metil hypoxanthine, 2-metil adenin
Example: Theophylline (tea), theobromine (chocolate), caffeine (coffee), uric acid (the result
of purine base metabolism

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Pyrimidine bases
The main ones in nucleotides: Uracil, Cytosine, Thymine
In tRNA: dihydrourasil, 5-methyl cytosine, 4-thio uracil (5 methyl cytosine in plant DNA, in
the tt cytosine virus is replaced with 5 hydroxy methyl cytosine)

Nucleoside
Compounds that are formed between pyrimidine purine base bonds and sugar (generally ribose
or deoxyribose) in N9 (purine), and N1 (pyrimidine) with b glycosidic bonds in C1 which are
in the N-glycosyl bond. For natural nucleosides: b glycosidic C1 furanose with N1 / N9 alkaline
pyrimidine purines

Bases in RNA (ribose): adenosine (A), guanosine (G), cytidine (C)

Base on DNA (deoxyribose): deoxy adenosine (dA), deoxy guanosine (dG), cytidine deoxy
(dC)
There is no T in the RNA (the number is very small), so that the RNA T is replaced by U
(Urasil / Uridin)

Adenila

Guanila

Cytodila

Unidila

Nucleoside properties:
1. More soluble than the N base
2. Stable in an alkaline atmosphere
3. In an acidic and high temperature atmosphere, hydrolyzed nucleosides become alkaline +
pentose
4. Pyrimidine nucleosides are more resistant to hydrolysis than nucleoside pyrin
5. Can be hydrolyzed by nucleosidase

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Nucleotides
Is a phosphoric acid ester with nucleosides (generally with C number 5 atoms called
nucleosides 5 phosphates)
In ribose there are 3 places (C2, C3, C5) while in deoxyribose there are 2 places (C3, C5), to
form phosphate esters. In the dominant biological tissue is C5.
Nucleotides of nucleic acid parts:
AMP: adenosine monophosphate, the acid is called adenylate acid = A
dAMP: deoxy adenosine monophosphate, the acid is called adenylate deoxy = dA
Based on the aount of phosphate group, nucleotide classified into:
• Nucleotide monophosphate (NMP)
• Nucleotide diphosphate (NDP): example: UDP (Uridine diphosphate), ADP(Adenosine
diphosphate), CDPCholine (Cystidine diphosphate choline)
Nucleotides are also classified into nucleotides nucleic acid and free nucleotides.
Free Nucleotides
Functions
1. Energy carrier molecules in cells, transfer energy (pirophosphate). Example: ATP, UTP,
GTP, CTP.
2. Reactive group carrier molecules. Example: UDP-UDPG: donor of glucose in glycogen
biosynthesis; CDP choline
3. Coenzyme section, for example FAD
4. Metabolic regulators, for example cAMP

UDP
glucose

The Structure of UDPG

Nucleotides in cells
• AMP CMP GMP UMP
• ADP CDP GDP UDP
• ATP CTP GTP UTP
• dAMP dCMP dGMP dUMP
• dADP dCDP dGDP dUDP
• dATP dCTP dGTP dUTP
• cAMP cCMP cGMP cUMP

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 Judging from the number of nucleotides
• Mononucleotides
Nicotinamide mononucleotide (NMN) Flavin mononucleotide (FMN)

• Dinucleotide
Nicotinamide Adenine Dinucleotide (NAD)
Flavin Adenine Dinucleotide (FAD)

Pirophosphate chain

• Polynucleotides: DNA and RNA

Polinucleotides
• Nucleic acids in the cell nucleus (especially chromatin): DNA, the nucleus contains DNA,
RNA
• Nucleic acids in the cytoplasm (especially ribosomes): RNA, in mitochondria: RNA and
DNA
• Eukaryotic DNA: DNA of the nucleus, cytoplasm, and membrane
• Repeating units in nucleic acids are nucleotides, in the form of "monophosphate
nucleosides"

DNA
• Polymers from: dA, dG, dT, dC
• Consists of 200,000 mononucleotides

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• Types of DNA based on different levels of monomers:
Humans, in E. coli (eukaryotic) dA + dT = dC + dG
dA + dT > dC + dG (yeast)
dA + dT < dC + dG (bacteria)
• Available in the cell nucleus (nucleoid), genetic material, mitochondria, cytoplasm
(plasmid), mesosoma membrane
• Consists of 2 strands in the form of double helices (spiral double-Watson & Crick), between
2 spirals there is a hydrogen bond.
• Three hydrogen bonds between dG and dC, 2 hydrogen bonds between dA and dT; with
the opposite spiral direction.
• There are 3 main forms of DNA: B, Z, A
• DNA direction (B): rotate right (right handed double helix)
• Polarity of 2 antiparallel molecular threads:
▪ Directions 5 → 3 (top to bottom): anti sense
▪ Direction 3 → 5 (top to bottom): sense / information carrier
Anti sense (5 → 3) is a complement / pair of sense
• Genetic information stored in DNA has 2 functions:
1) Information on protein transcription
2) Information derived in replication

Genetic information stored in DNA has 2 functions:

1) Information on protein transcription
2) Information derived in replication

Helix diameter = 20A; the distance between adjacent bases = 3.4 A; each helix round consists
of 10 base pairs. So that the total base distance is 34 A.
• Form B: physiological condition, the main form of DNA in cell DNA, right rotating helix,
every round of 10 base pairs
• Form Z: left rotating helix, each round 12 base pairs, occurs between bonds due to base
methylation, in the inactive gene.

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• Form A: form B is dehydrated; shorter than B every 11 pairs of pairs

RNA
• Consists of 5000-50,000 nucleotides
• Polymers from: Uridilat (U), Sitidylate (C), Adenilat (A), Guanilat (G)
• Phosphodiester bond = on DNA (3,5-phosphodiester)
• T is replaced by U; a small portion is thymidylate on the tRNA
Types of RNA based on size, function, stability
• mRNA = messenger RNA = ambassador RNA = messenger = carrier of genetic information
• tRNA = transfer of RNA = adapter / adjustment for translation from information on the
order of the mRNA nucleotide to the amino acid sequence
• tRNA moves / carries amino acids to a protein synthesis tool
• rRNA = ribosomal RNA; place of protein formation in the ribosome
• mRNA, tRNA, rRNA: present in prokaryotic and eukaryotic cells; in eukaryotics there are
2 other types:
1) hnRNA = heterogenous nuclear RNA: heterogeneous and large RNA set as the
beginning of mRNA
2) snRNA = small nuclear RNA. It plays a role in changing hnRNA to mRNA. Role in the
signal to release proteins that will be secreted
Charectiristics:
Pentose: ribose
• It consists of 1 thread (although it is able to hold folds with opposite polarity, but not
helices). Then the concentration of G C or A U
• Complement of DNA sense
• Can be hydrolyzed by alkali → intermediate 2,3 cyclic nucleoside monophosphate →
ekimolar mixture of 2 nucleoside monophosphate + 3 nucleoside monophosphate
(reaction). Intermediates are not formed in the DNA hyd

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• RNA is synthesized in the cell nucleus through "transcription" of 1 strand of DNA, with
the RNA polymerase enzyme → single chain RNA → modification before performing its
function. Processing in the nucleus and cytoplasm → tRNA, rRNA, mRNA.
In eukaryotic cells there are 3 RNA polymerases
1. RNA polymerase I, in the nucleus (nucleus) -> is responsible for rRNA synthesis
2. RNA polymerase II, in nucleoplasm / nucleus plasma -> for hnRNA synthesis
3. Polymerase III, in nucleoplasm -> for tRNA synthesis.
MtRNA polymerase, in mitochondria -> for the synthesis of tRNA, mRNA, and rRNA
DNA to RNA Transcription

mRNA: hnRNA that has undergone maturation / modification in the cell nucleus; then sent to
the cytoplasm as mRNA.
Modification:
1) Closed formation (formation at the end of 5: 7 methyl guanosine triphosphate) has an effect
on determining the first codon of AUG
2) Tailed poly (Formation at the tip 3: adenylate polymer) functions to maintain stability
tRNA
• Contains 75 nucleotides and contains unusual bases
• Transport of active amino acids
• Called adapters or adjustments that play a role in adjusting amino acids with mRNA codons
• Modification, in the nucleus and cytoplasm
1. Methylation
2. Cleavage and folding, partially partial trait
3. Anti codon preparation
4. Formation of a typical place for one amino acid, namely the ACC at the 3 'end, and G
at the 5' end

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Each amino acid has one or more suitable tRNA molecules as carriers of amino acids, in the
process of protein biosynthesis. If there are 20 acid-forming amino acids, there is a minimum
of 20 kinds of tRNA in each cell.
In protein biosynthesis:
Activation of amino acids by ATP → aminosil tRNA
Brought to the ribosome, transferred to the polypeptide chain to form proteins
The first codon of mRNA: AUG → anticodon AUC on tRNA → tRNA carrying amino acids
Codon Table

rRNA
• rRNA + protein → complex: ribosom
• Contains 3 main bases: A, G, C, U and several transmetylation bases

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• Eukaryotic cell ribosomes of S (Svedberg) value = 80, consisting of 2 subunits which are
not equal: 60S and 40S
• 60S sub-unit: there are 3 kinds of rRNA
40S sub-unit: there is 1 kind of rRNA

Nucleic Acid Hydrolysis

1. Acid (pH=3)
a. Breaking b-glycosidic bonds of purine bases and ribose deoxy. Whereas pyrimidine
with ribose deoxyose, the bonds between menonucleotide units do not change (the DNA
that remains does not contain purines) is called apurinic acid
b. Added 12 M HCLO4, a strong oxidizing agent (100°C, 1 hour) →phosphodiester bond
→ ribose base, phosphate
2. Base
DNA: not in action
RNA: positive (because there is OH on C2) Formation of 2,3-cyclic nucleoside mono
phosphate -> 3 nucleoside monosfat + 2 nucleoside monophosphate
3. Enzyme
Endonuclease: randomly on the phosphodiester bridge, part of the polypetide chain. For
example cow pancreatic ribonuclease, results: cyclic phosphate
Exonuclease: at the ends of the polypetide chain. For example snake venom
phosphodiesterase, hydrates the bond between phosphoric and hydroxyl acids 3 '→ results:
nucleoside 5' phosphate