5. NUCLEIC ACIDS5. NUCLEIC ACIDS

Medical BiochemistryMedical BiochemistryMolecular Principles of Structural Organization of CellsMolecular Principles of Structural Organization of Cells

COMPONENTS OF THE NUCLEIC ACIDSCOMPONENTS OF THE NUCLEIC ACIDS

1. NITROGENOUS BASES1. NITROGENOUS BASES

The nitrogenous bases are divided into two groups:The nitrogenous bases are divided into two groups:1. 1. Purine bases:Purine bases:

PurinePurine Adenine (A, Ade) Adenine (A, Ade) Guanine (G, Gua) Guanine (G, Gua) 6-aminopurine6-aminopurine 2-amino-6-oxopurine2-amino-6-oxopurine

2. 2. Pyrimidine basesPyrimidine basesPyrimidinePyrimidine Uracil (U, Ura)Uracil (U, Ura) Thymine (T, Thy) Cytosine (C, Thymine (T, Thy) Cytosine (C, Cyt)Cyt)

2,4-dioxypyrimidine 2,4-dioxypyrimidine 5-methyluracil 5-methyluracil 2-oxo-4- 2-oxo-4-aminopyrimidineaminopyrimidine

N

N NH

N

NH2

H2N

HN

N NH

N

ON

N NH

N1

23

4

56

7

8

9

N

N1 6

54

3

2

NH

N

NH2

ONH

HN

O

O NH

HN

O

O

CH3

Nitrogenous bases (NB) are classified inNitrogenous bases (NB) are classified in::

Major basesMajor basesMajor Major purine purine bases are bases are – Adenine (A)Adenine (A)

was isolated from pancreas and yeast was isolated from pancreas and yeast in both DNA and RNA, in nucleosides mono-, di-, triphosphates, coenzymesin both DNA and RNA, in nucleosides mono-, di-, triphosphates, coenzymes

– Guanine (G)Guanine (G)isolated from guanoisolated from guanoin both DNA and RNA, nucleosides mono-, di-, triphosphatesin both DNA and RNA, nucleosides mono-, di-, triphosphates

Major Major pyrimidinepyrimidine bases are bases are – Uracil (U)Uracil (U)

in RNA, nucleotides, activates the substrates (UDP-glucose), freein RNA, nucleotides, activates the substrates (UDP-glucose), free

– Thymine (T)Thymine (T)isolated from thymus DNAisolated from thymus DNAin DNA, and in small amounts in RNAin DNA, and in small amounts in RNA

– Cytosine (C) Cytosine (C) in both DNA and RNA, nucleosides (cytidin-phosphates) acting in the synthesis in both DNA and RNA, nucleosides (cytidin-phosphates) acting in the synthesis of phospholipidsof phospholipids

Minor basesMinor bases are primarily found in tRNA and in trace in rRNA; e.g.: are primarily found in tRNA and in trace in rRNA; e.g.:

2-methyladenine, 1-methylguanine, 5-methylcytosine, 5-oxymethylcytosine2-methyladenine, 1-methylguanine, 5-methylcytosine, 5-oxymethylcytosine

General properties of the nitrogenous basesGeneral properties of the nitrogenous bases

They are hetero-cycles; due to the presence of N have an alkaline characterThey are hetero-cycles; due to the presence of N have an alkaline character

When H is changed with –OH or –NHWhen H is changed with –OH or –NH22 the solubility in water is reduced, the melting the solubility in water is reduced, the melting point increasespoint increasesThe bases have the ability to undergo a lactam-lactim (keto-enol) tautomerismThe bases have the ability to undergo a lactam-lactim (keto-enol) tautomerism

The amine compounds have an alkaline character, the enol compounds act as acids.The amine compounds have an alkaline character, the enol compounds act as acids.At pH<9 (in biological systems) the lactam (keto) form is predominant favoring the At pH<9 (in biological systems) the lactam (keto) form is predominant favoring the formation of covalent bonds of N-glycoside type between N atom in position 1 of formation of covalent bonds of N-glycoside type between N atom in position 1 of pyrimidine or N atom in position 9 of purine and semiacetal –OH (C-1) of pentosepyrimidine or N atom in position 9 of purine and semiacetal –OH (C-1) of pentoseThey have a maximum absorbance at They have a maximum absorbance at =260nm (UV) – used to dose with =260nm (UV) – used to dose with spectrophotometric method in UVspectrophotometric method in UVLow solubility in cold water; soluble in alkaline solutionsLow solubility in cold water; soluble in alkaline solutions

NH

HN

O

O N

N

OH

HO

2. PENTOSES2. PENTOSES-Ribose (R)-Ribose (R) -2-deoxyribose (dR)-2-deoxyribose (dR)

in RNAin RNA in DNAin DNA

3. PHOSPHORIC ACID MOIETY3. PHOSPHORIC ACID MOIETYHH33POPO44 - PO- PO33HH22

- is able to link the nucleotides forming phosphodiester bond between is able to link the nucleotides forming phosphodiester bond between -OH in position 3’ of the pentose in one nucleotide and -OH in position 3’ of the pentose in one nucleotide and -OH in position 5’ in the other nucleotide-OH in position 5’ in the other nucleotide

OHPHO

OH

O

CH2-OH

H

OH

H

OH OH

H HO

CH2-OH

H

OH

H

OH H

H HO

OHP

OH

O

Compounds containing nitrogenous base linked to pentose = Compounds containing nitrogenous base linked to pentose = nucleosidesnucleosides(C-1’ of pentose is linked to N-9 in purine or N-1 in pyrimidine = (C-1’ of pentose is linked to N-9 in purine or N-1 in pyrimidine = N-N--glycosidic bond-glycosidic bond))RibonucleosidesRibonucleosidesR+ A = adenosineR+ A = adenosine R+ G = guanosine R+ G = guanosine R+ C = cytidine R+ C = cytidine R+ U = uridine R+ U = uridine

DeoxyribonucleosidesDeoxyribonucleosidesdR+A=deoxyadenosine dR+G=deoxyguanosine dR+C=deoxycytidine dR+T=deoxythymidinedR+A=deoxyadenosine dR+G=deoxyguanosine dR+C=deoxycytidine dR+T=deoxythymidine

NUCLEOSIDES

N

N N

N

NH2

O

OHOH

HHH

CH2

H

HOO

OHOH

HHH

CH2

H

HO

HN

N N

N

O

H2N

O

OHOH

HH

H

CH2

H

HO

N

N

NH2

O

O

OHOH

HH

H

CH2

H

HO

HN

N

O

O

N

N N

N

NH2

O

HOH

HHH

CH2

H

HOO

HOH

HHH

CH2

H

HO

HN

N N

N

O

H2N

O

HOH

HH

H

CH2

H

HO

N

N

NH2

O

O

HOH

HH

H

CH2

H

HO

HN

N

O

O

CH3

NUCLEOSIDESNUCLEOSIDES

Are considered products of the partial hydrolysis of nucleotidesAre considered products of the partial hydrolysis of nucleotides

Ribonucleosides exist free in small amounts; deoxyribonucleosides do Ribonucleosides exist free in small amounts; deoxyribonucleosides do not exist free not exist free

Minor nucleosidesMinor nucleosides contain minor nitrogenous bases contain minor nitrogenous basesexist in tRNAexist in tRNAthe most widespread are dihydrouridine, pseudouridine, ribothymidinethe most widespread are dihydrouridine, pseudouridine, ribothymidine

NUCLEOTIDESNUCLEOTIDES • They are the monomer units of the nucleic acids; they result from the partial hydrolysis of the nucleic acids under the action of nucleases• They are phosphoric esters of the nucleosides (nucleotide = nucleoside + H3PO4 = nitrogenous base + pentose + H3PO4)• The phosphate group can add to positions 2’, 3’, 5’ of ribose

3’, 5’ of deoxyribose

adenosine-3’-monophosphate adenosine-5’-monophosphate

• Free nucleotides are nucleosides-5’-P (mononucleotides) that are involved in the synthesis of nucleic acids and are formed by their decomposition

O

OHOH

HH

H

CH2

H

OPHO

OH

O

N

N N

N

NH2

O

OHO

HHH

CH2

H

PO

OH

HO

OH

N

N N

N

NH2

Ribomononucleotides R+A+H3PO4 = adenosine-5’-monophosphate = AMP = adenylic acidR+G+H3PO4 = guanosine-5’-monophosphate = GMP = guanylic acidR+C+H3PO4 = cytidine-5’-monophosphate = CMP = cytidylic acidR+U+H3PO4 = uridine-5’-monophosphate = UMP = uridylic acid

DeoxyribomononucleotidesdR+A+H3PO4 = deoxyadenosine-5’-monophosphate = dAMP = deoxyadenylic aciddR+G+H3PO4 = deoxyguanosine-5’-monophosphate = dGMP = deoxyguanylic aciddR+C+H3PO4 = deoxycytidine-5’-monophosphate = dCMP = deoxycytidylic aciddR+T+H3PO4 = deoxythymidine-5’-monophosphate = dTMP = deoxythymidylic acid

O

OHOH

HH

H

CH2

H

OPHO

OH

O

N

N N

N

NH2

O

OH

HHH

CH2

HOH

OPHO

OH

OH

HN

N N

N

O

H2N

O

OH

HH

H

CH2

H

N

N

NH2

O

OH

OP

O

OH

HO O

OHOH

HH

H

CH2

H

HN

N

O

O

OPHO

O

OH

O

HOH

HH

H

CH2

H

OPHO

OH

O

N

N N

N

NH2

O

H

HHH

CH2

HOH

OPHO

OH

OH

HN

N N

N

O

H2N

O

H

HH

H

CH2

H

N

N

NH2

O

OH

OP

O

OH

HOO

HOH

HH

H

CH2

H

HN

N

O

O

OPHO

O

OH

CH3

NucleosideNucleosidepolypolyphosphatesphosphates are formed by linking an additional are formed by linking an additional phosphate group. phosphate group.

The nucleotides may contain – 1 phosphoric acid moiety - mononucleotides (monophosphate nucleosides),

– 2 phosphoric acid moieties - dinucleotides (diphosphate nucleosides),

– 3 phosphoric acid moieties - trinucleotides (triphosphate nucleosides),

Nucleoside diphosphates and triphosphates are the most frequently occuring Nucleoside diphosphates and triphosphates are the most frequently occuring in the cells. in the cells.

In the cell, all the nucleoside phosphates occur as anions:AMP2-, ADP3-, ATP3-

ADP and ATP are rich in energy = macroergic, used by the organism for performing different functions.

Other nucleotides are implicated in the function of biological synthesis.

Ribonucleoside phosphatesRibonucleoside phosphates

adenosine-5’-mono-, di-, tri-phosphate = AMP, ADP, ATPguanosine-5’-mono-, di-, tri-phosphate = GMP, GDP, GTPcytidine -5’-mono-, di-, tri-phosphate = CMP, CDP, CTPuridine -5’- mono-,di-, tri-phosphate = UMP, UDP, UTP

AMPAMP ADP ADP ATP ATP

Deoxyribonucleosides phosphatesDeoxyribonucleosides phosphatesdeoxyadenosine-5’- mono-, di-, tri-phosphate = dAMP, dADP, dATPdeoxyguanosine-5’- mono-, di-, tri-phosphate = dGMP, dGDP, dGTPdeoxycytidine -5’- mono-, di-, tri-phosphate = dCMP, dCDP, dCTPdeoxythymidine-5’- mono-, di-, tri-phosphate = dTMP, dTDP, dTTP

O

OHOH

HH

H

CH2

H

OPHO

OH

O

N

N N

N

NH2

O

OHOH

HHH

CH2

H

OPO

OH

N

N N

N

NH2

O

P

OH

O

O

P

OH

HO

O

O

OHOH

HHH

CH2

H

OPO

OH

N

N N

N

NH2

O

P

OH

HO

O

NUCLEOTIDE DERIVATIVESNUCLEOTIDE DERIVATIVES

Cyclic nucleotides Cyclic nucleotides (3’,5’-AMP(3’,5’-AMPcc 3’,5’-GMP 3’,5’-GMPcc) are universal regulators of intracellular metabolism. ) are universal regulators of intracellular metabolism. – cAMP cAMP

is mediator of the action of hormones as second messenger, is mediator of the action of hormones as second messenger, activates and regulates the function of enzymes – allosteric mechanism in metabolic activates and regulates the function of enzymes – allosteric mechanism in metabolic systems.systems.

– cGMP cGMP Second messenger for the action of hormonesSecond messenger for the action of hormones

cAMPcAMP cGMPcGMP

O

OHO

HHH

CH2

HPO

OH

O

N

N N

N

NH2

O

OH

HHH

CH2

HOP

OH

O

HN

N N

N

O

H2N

O

NUCLEOTIDE DERIVATIVESNUCLEOTIDE DERIVATIVESNucleotide coenzymesNucleotide coenzymes (uridine, cytidine, deoxythymidine, adenosine, guanosine coenzymes) contain residues of glucides, alcohols, aminoacids, lipids, (uridine, cytidine, deoxythymidine, adenosine, guanosine coenzymes) contain residues of glucides, alcohols, aminoacids, lipids,

inorganic compounds:inorganic compounds:UDP-glucose (UDPGlc, UDPGUDP-glucose (UDPGlc, UDPG) is intermediate in the reversible conversion of glucose in galactose, formation of glycogen in animals or starch in plants.) is intermediate in the reversible conversion of glucose in galactose, formation of glycogen in animals or starch in plants.CDP-choline CDP-choline is involved in the formation of phosphatidyl-choline and choline plasmalogensis involved in the formation of phosphatidyl-choline and choline plasmalogensCMP-sialic acidCMP-sialic acidUDP-glucuronic acidUDP-glucuronic acid is a donor of glucuronic acid radical for the coupling reactions of native or foreign substances is a donor of glucuronic acid radical for the coupling reactions of native or foreign substances

UDP-GUDP-G CDP-cholineCDP-choline

O

OHOH

HH

H

CH2

H

HN

N

O

O

OPO

O

OH

P

OH

OH O

OH OH

OHH

OH

CH2-OH

HH

O

OH

HH

H

CH2

H

N

N

NH2

O

OH

OP

O

OH

OP

OH

O

O

H2CH2CN+

CH3

H3C

CH3

GENERAL PROPERTIES AND BIOCHEMICAL ROLE GENERAL PROPERTIES AND BIOCHEMICAL ROLE OF NUCLEOTIDESOF NUCLEOTIDES

Properties:Properties:– Have an Have an acidicacidic character (the protons in the phosphoric acid moiety character (the protons in the phosphoric acid moiety

dissociate: nucleozid-O-POdissociate: nucleozid-O-PO332-2-))

– Maximum Maximum absorbance at absorbance at =260nm=260nm (UV) due to the presence of (UV) due to the presence of nitrogenous basesnitrogenous bases

– Nucleotides can be hydrolyzed by Nucleotides can be hydrolyzed by 5’-nucleotidase5’-nucleotidase, setting the H, setting the H33POPO44 freefree

Biochemical role:Biochemical role:– In the structure of coenzymes (NADIn the structure of coenzymes (NAD++, FAD, CoA-SH), FAD, CoA-SH)– Coenzymes: UDP-G, CDP-CholineCoenzymes: UDP-G, CDP-Choline– Take part in the enzyme catalyzed reactions:Take part in the enzyme catalyzed reactions:

CTP biosynthesis of phospholipidsCTP biosynthesis of phospholipidsUTP in biosynthesis and conversion of carbohydratesUTP in biosynthesis and conversion of carbohydrates

– Trinucleotides are precursors in the biosynthesis of nucleic acidsTrinucleotides are precursors in the biosynthesis of nucleic acids– Second messengers for the hormonal control (3’5’-AMPc, 3’5’-GMPc)Second messengers for the hormonal control (3’5’-AMPc, 3’5’-GMPc)– ATP is the universal macroergic compound of living organismsATP is the universal macroergic compound of living organisms

Role and biochemical importance of ATPRole and biochemical importance of ATPATP, ADP, AMP take part in processes of storage and utilization of the energy set ATP, ADP, AMP take part in processes of storage and utilization of the energy set free during the cellular metabolismfree during the cellular metabolismThey act as donors or acceptors of phosphate moietyThey act as donors or acceptors of phosphate moietyThe reaction: ATP-aseThe reaction: ATP-ase

ATP + HATP + H22O ADP + HO ADP + H33POPO44

reflects the energy flow in the cell; it provides the transfer of the chemical energy used in reflects the energy flow in the cell; it provides the transfer of the chemical energy used in the cellular metabolism. the cellular metabolism.

This process implies 2 fundamental aspects:This process implies 2 fundamental aspects:1.1. Formation of ATP represents the Formation of ATP represents the storagestorage of chemical energy resulted from the of chemical energy resulted from the

food food 2.2. Transformation of ATP in ADP represents the Transformation of ATP in ADP represents the generation and usegeneration and use of energy of energy

stored in the ATP moleculestored in the ATP molecule

ATPATP ADP ADP HH33POPO44

O

OHOH

HHH

CH2

H

OPO

OH

N

N N

N

NH2

O

P

OH

O

O

P

OH

HO

O +H2O

-H2O

generation of energy

accumulation of energy

OHPHO

OH

O

O

OHOH

HHH

CH2

H

OPO

OH

N

N N

N

NH2

O

P

OH

HO

O

POLYNUCLEOTIDES = NUCLEIC ACIDSPOLYNUCLEOTIDES = NUCLEIC ACIDS

Are macromolecular substances result of the condensation of a great Are macromolecular substances result of the condensation of a great number of mononucleotides (structural units)number of mononucleotides (structural units)

They are:They are:– Polyribonucleotides Polyribonucleotides = = Ribonucleic acid (RNA)Ribonucleic acid (RNA)– Polydeoxyribonucleotides Polydeoxyribonucleotides = = Deoxyribonucleic acid (DNA)Deoxyribonucleic acid (DNA)

Distinct characters:Distinct characters: DNADNA RNARNA

NB:NB: A, G, C, A, G, C, TT A, G, C, A, G, C, UUPentose:Pentose: dRdR RRNumber of nucleotide monomersNumber of nucleotide monomers DNADNA >> RNARNALength of chainLength of chain DNADNA > (except some > (except some

viruses)viruses)StructureStructure double helixdouble helix 1 chain1 chain

Due to the acidic character, nucleic acids are linked with basic proteins, Due to the acidic character, nucleic acids are linked with basic proteins, (histones and protamines) and neutal proteins forming (histones and protamines) and neutal proteins forming

deoxyribo-nucleoproteinsdeoxyribo-nucleoproteins ribonucleoproteinribonucleoprotein

STRUCTURE AND LEVELS OF ORGANIZATION STRUCTURE AND LEVELS OF ORGANIZATION OF NUCLEIC ACIDSOF NUCLEIC ACIDS

PRIMARY STRUCTUREPRIMARY STRUCTURE

DNA and RNA are DNA and RNA are linear polynucleotide chainlinear polynucleotide chain made up of made up of mononucleotides linked by mononucleotides linked by 3’,5’-phosphodiester bonds3’,5’-phosphodiester bonds: : each pentose 3’-OH of one mononucleotide is linked each pentose 3’-OH of one mononucleotide is linked covalently to pentose 5’-OH of the neighboring covalently to pentose 5’-OH of the neighboring mononucleotide. mononucleotide.

The chains have 2 ends: The chains have 2 ends: 5’ end5’ end with triphosphate with triphosphate and and 3’ end3’ end with a free –OH with a free –OH

The chains are The chains are polarpolar and directed 5’ and directed 5’ 3’ or 3’ 3’ or 3’ 5’ (exception: 5’ (exception: the circular DNA and RNA of certain viruses and bacteria).the circular DNA and RNA of certain viruses and bacteria).

STRUCTURE AND LEVELS OF ORGANIZATION STRUCTURE AND LEVELS OF ORGANIZATION OF NUCLEIC ACIDSOF NUCLEIC ACIDS

PRIMARY STRUCTUREPRIMARY STRUCTURE

The genetic text of DNA is composed of The genetic text of DNA is composed of code tripletscode triplets or or codonscodons = linear sequences of three adjacent = linear sequences of three adjacent nucleotidesnucleotides

The sites of DNA chain that contains information on The sites of DNA chain that contains information on the primary structure of all types of RNA are the primary structure of all types of RNA are structural genes. structural genes.

The order of nucleotides in RNA is the same as that in The order of nucleotides in RNA is the same as that in the DNA region that is replicated (copied) with the the DNA region that is replicated (copied) with the distinction that RNA consists of ribonucleotides that distinction that RNA consists of ribonucleotides that contain U instead of Tcontain U instead of T

O

HO

HHH

CH2

H

OPHO

OH

O

O

H

HHH

CH2

HO

O

PHO

O

H

HH

H

CH2

H

N

N

NH2

O

O

O

PHO

O

HO

HH

H

CH2

H

HN

N

O

O

O

P

HO

O

N

N N

N

NH2

HN

N N

N

O

H2N

CH3

O

O

5'

5'

5'

5'

3'

3'

3'

3'

O

OHO

HHH

CH2

H

OPHO

OH

O

O

OH

HHH

CH2

HO

O

PHO

O

OH

HH

H

CH2

H

N

N

NH2

O

O

O

PHO

O

OHO

HH

H

CH2

H

HN

N

O

O

O

P

HO

O

N

N N

N

NH2

HN

N N

N

O

H2NO

O

5'

5'

5'

3'

3'

3'

3'

5'

Primary structure of DNA Primary structure of RNA

3’.5’-phosphodiester bond

3’.5’-phosphodiester bond

3’.5’-phosphodiester bond

3’.5’-phosphodiester bond

3’.5’-phosphodiester bond

3’.5’-phosphodiester bondA

G

C

T

SECONDARY STRUCTURESECONDARY STRUCTUREIn 1953 In 1953 Watson and Watson and CrickCrick proposed a proposed a double-helix modeldouble-helix model for for the DNA secondary the DNA secondary structurestructureThe chains are directed The chains are directed antiparallelly antiparallelly (one chain (one chain runs in runs in 5’5’ 3’ direction 3’ direction and the second 3’ and the second 3’ 5’ 5’ direction)direction)The pentose phosphate The pentose phosphate moieties are directed moieties are directed outwards outwards The bases protrude into The bases protrude into the interior of the helixthe interior of the helix

Formed by specific pairing of a base of one polynucleotide Formed by specific pairing of a base of one polynucleotide chain with a base of the other chain. The correspondence of chain with a base of the other chain. The correspondence of the base pairs is called the base pairs is called complementaritycomplementarity– The interaction of A and T is effected through the The interaction of A and T is effected through the

involvement of 2 H bondsinvolvement of 2 H bonds– The interaction of G and C is effected through the The interaction of G and C is effected through the

involvement of 3 H bondsinvolvement of 3 H bonds

A = TA = T G G ≡ ≡ CC

NN

O

O

CH3

N

NN

N

NH H

H

H

HN

N

N

O

NN

NN

N

OH

H

H

H

H

H

H

H

SECONDARY STRUCTURE OF DNASECONDARY STRUCTURE OF DNA

Relationship concerning the content of individual bases in DNA Relationship concerning the content of individual bases in DNA (Chargaff, 1949):(Chargaff, 1949):

1.1. A+G = C+T A+G = C+T or (A+G)/(C+T) = 1or (A+G)/(C+T) = 1

2.2. A = TA = T or A/T = 1or A/T = 1

3.3. G = CG = C or G/C =1or G/C =1

4.4. A+C = G+T A+C = G+T or 6-amino group = 6-keto group or 6-amino group = 6-keto group

5.5. (A+T) and (G+C) are the only variable; if:(A+T) and (G+C) are the only variable; if:

(A+T)>(G+C) the DNA is AT type(A+T)>(G+C) the DNA is AT type

(G+C)>(A+T) the DNA is GC type(G+C)>(A+T) the DNA is GC type

These rules indicate that the buildup of DNA is effected in a These rules indicate that the buildup of DNA is effected in a strict conformity with the pairwise interactions A-T and G-Cstrict conformity with the pairwise interactions A-T and G-C

TERTIARY STRUCTURE OF DNATERTIARY STRUCTURE OF DNA

The double helical molecule is twisted looking like a The double helical molecule is twisted looking like a supercoil or a bent double-helixsupercoil or a bent double-helix

It has a great flexibility; the conformation is not rigid.It has a great flexibility; the conformation is not rigid.

There are differences between the native DNA, ”in vivo”, There are differences between the native DNA, ”in vivo”, and the one “in vitro”; by removing the water and and the one “in vitro”; by removing the water and dependent on the electrolytes in the environment, the dependent on the electrolytes in the environment, the double-helix is structurally altered.double-helix is structurally altered.

TYPES AND LOCATION OF DNATYPES AND LOCATION OF DNA

Nuclear DNANuclear DNA (97-98%) in the chromosomes coupled with (97-98%) in the chromosomes coupled with basic proteins (protamines, histones) forming chromatine. basic proteins (protamines, histones) forming chromatine. NucleolusNucleolus contains associated DNA and RNA contains associated DNA and RNA

Mitochondrial DNAMitochondrial DNA (1-3%) in the mitochondria matrix (1-3%) in the mitochondria matrix– Structure of simple or double circular helix; does not form Structure of simple or double circular helix; does not form

complex with proteins; MW << nuclear DNAcomplex with proteins; MW << nuclear DNA– Function:Function:

Takes part in maintenance of the mitochondria structureTakes part in maintenance of the mitochondria structure

Contains the information necessary to synthesize Contains the information necessary to synthesize specific proteins intra and extra mitochondriaspecific proteins intra and extra mitochondria

May control the synthesis of the ribosomesMay control the synthesis of the ribosomes

Site of the genetic mutationsSite of the genetic mutations

GENERAL PROPERTIES OF DNAGENERAL PROPERTIES OF DNA

1.1. COLLOIDAL BEHAVIORCOLLOIDAL BEHAVIOR

On dissolution, nucleic acids become swollen and form On dissolution, nucleic acids become swollen and form viscousviscous, colloid-like solutions; the , colloid-like solutions; the hydrophilicityhydrophilicity is mainly is mainly determined by the occurrence of phosphate moieties; in determined by the occurrence of phosphate moieties; in solution the nucleic acids exist as solution the nucleic acids exist as polyanions polyanions with acidic with acidic properties. Double-stranded nucleic acids are less soluble properties. Double-stranded nucleic acids are less soluble than single-stranded onesthan single-stranded ones

2.2. DENATURATION - RENATURATIONDENATURATION - RENATURATION

Is produced by heating and the action of chemical agents Is produced by heating and the action of chemical agents which which break hydrogen and van der Waals bonds stabilizing break hydrogen and van der Waals bonds stabilizing the secondary and tertiary structuresthe secondary and tertiary structures. E.g.: heating DNA . E.g.: heating DNA results in a separation of its double helix results in a separation of its double helix (“helix-coil” transition); (“helix-coil” transition);

Slowly cooled, the chains reunite according to the Slowly cooled, the chains reunite according to the complementarity principle, DNA regaining its native double–complementarity principle, DNA regaining its native double–helix; this phenomenon is called helix; this phenomenon is called renaturationrenaturation

The helical structure rotate the plane of polarized light exhibiting an optical activity while the breakdown of the spatial arrangement reduce the optical activity to zero.

The DNA absorbs the UV light maximally at 260nm. The absorption intensity of a native nucleic acid is

increased as the DNA is denaturated (hyperchromic effect) or

decreased when the double-helix is reformed (hypochromic effect)

3. HYBRIDIZATION: the process whereby hybrid duplexes of complementary DNA and RNA combined.the aptitude of nucleic acid to renaturate after denaturation has provided a valuable method of cloning different genes and other DNA sequences from different organisms

BIOLOGICAL FUNCTIONS OF DNABIOLOGICAL FUNCTIONS OF DNA

The molecular basis of the transmission of genetic information The molecular basis of the transmission of genetic information from one generation to anotherfrom one generation to another

Ensures and controls the synthesis of the proteins (enzymes)Ensures and controls the synthesis of the proteins (enzymes)

In DNA there is encoded the genetic program of development, In DNA there is encoded the genetic program of development, maintenance and reproduction of each organismmaintenance and reproduction of each organism

Ensures the differentiation and regulation of cells and the Ensures the differentiation and regulation of cells and the constance of the cell replicationconstance of the cell replication

Is the molecular basis of the natural or induced genetic Is the molecular basis of the natural or induced genetic mutationsmutations

STRUCTURE AND LEVELS OF ORGANIZATION OF STRUCTURE AND LEVELS OF ORGANIZATION OF RNARNA

SECONDARY AND TERTIARY STRUCTURESECONDARY AND TERTIARY STRUCTURE

Messenger RNA = mRNAMessenger RNA = mRNA

Formed in the cell from pro-mRNA that contains the Formed in the cell from pro-mRNA that contains the transcripts of DNAtranscripts of DNA

The code element of mRNA is a linear sequence of three The code element of mRNA is a linear sequence of three adjacent nucleotides = codon or code triplet. Each codon adjacent nucleotides = codon or code triplet. Each codon corresponds to a defined aminoacid. corresponds to a defined aminoacid.

The secondary structure of mRNA is a The secondary structure of mRNA is a bent chain bent chain (hairpins (hairpins and linear regions)and linear regions)

The tertiary structure is like a thread wound round a spool The tertiary structure is like a thread wound round a spool (a special transport protein - informofer)(a special transport protein - informofer)

Transfer RNA = tRNATransfer RNA = tRNAThe secondary structure of tRNA is a shape of The secondary structure of tRNA is a shape of clover-leaf clover-leaf determined by determined by intrachain pairing of complementary nucleotides in certain regions of the intrachain pairing of complementary nucleotides in certain regions of the chain:chain:

1.1. Acceptor regionAcceptor region (end or terminus) - 4 linearly linked nucleotides of which (end or terminus) - 4 linearly linked nucleotides of which CCA sequence is common in all types of tRNA. The 3’ –OH of CCA sequence is common in all types of tRNA. The 3’ –OH of adenosine is free. At this site the -COOH of the aminoacid is added to be adenosine is free. At this site the -COOH of the aminoacid is added to be transported to the ribosomes, to be used in the protein synthesis.transported to the ribosomes, to be used in the protein synthesis.

2.2. Anticodon loopAnticodon loop (7 nucleotides) contains a triplet specific for each tRNA = (7 nucleotides) contains a triplet specific for each tRNA = anticodon, complementarily paired to a codon of mRNA; the interaction anticodon, complementarily paired to a codon of mRNA; the interaction betweencodon and anti-codon determines the order of the aminoacids in betweencodon and anti-codon determines the order of the aminoacids in the polypeptide chainthe polypeptide chain

3.3. Thymine-pseudouracil (TThymine-pseudouracil (TΨΨC) loopC) loop (7 nucleotides) involved in binding the (7 nucleotides) involved in binding the tRNA to the ribosometRNA to the ribosome

4.4. Dihydrouridine loop (diHU) (8-12 nucleotides) binding aminoacyl-t-RNA Dihydrouridine loop (diHU) (8-12 nucleotides) binding aminoacyl-t-RNA synthetase, the enzyme which recognizes the aminoacidsynthetase, the enzyme which recognizes the aminoacid

5.5. Extra loop varies in shape and composition in various tRNAExtra loop varies in shape and composition in various tRNAThe tertiary structure – shape of a bent elbow; the cloverleaf loops are The tertiary structure – shape of a bent elbow; the cloverleaf loops are folded back on the molecular framework and held together by Van der folded back on the molecular framework and held together by Van der Waals bondsWaals bonds

Ribosomal RNA = rRNARibosomal RNA = rRNAEnters in the structure of the ribosomes. Enters in the structure of the ribosomes.

n ribosomes + 1 mRNA = polisomen ribosomes + 1 mRNA = polisomeSecondary structure: helical regions alternating with Secondary structure: helical regions alternating with nonhelical bent regionsnonhelical bent regionsTertiary structure constitutes the framework for the Tertiary structure constitutes the framework for the ribosome; ribosomes proteins adhere to the tertiary ribosome; ribosomes proteins adhere to the tertiary structure on the outside.structure on the outside.

Chromosomal RNA in nucleus –recognition and activation of Chromosomal RNA in nucleus –recognition and activation of DNA genesDNA genes

Low-molecular RNA in nucleus and cytoplasmic RNA particles – Low-molecular RNA in nucleus and cytoplasmic RNA particles – activation of DNA genes formation of the skeleton for activation of DNA genes formation of the skeleton for protein particles involved in the transfer of rNA from protein particles involved in the transfer of rNA from nucleus into the cytoplasmnucleus into the cytoplasm