NUCLEINUCLEIC C

ACIDSACIDS

OBJECTIVESOBJECTIVES Identify/ recognize nucleic acidIdentify/ recognize nucleic acid Components in nucleic acid – Components in nucleic acid –

monosaccharide, nucleobases, monosaccharide, nucleobases, phosphoric acidphosphoric acid

Differentiate - between 2 types of Differentiate - between 2 types of nucleic acids, nucleic acids, DNA and RNADNA and RNA

- between nucleotide and - between nucleotide and

nucleosidenucleoside Definition – nucleotide, nucleoside, DNA Definition – nucleotide, nucleoside, DNA

and and RNA RNA

Nucleic AcidsNucleic Acids Nucleic acid:Nucleic acid: a biopolymer containing three types of a biopolymer containing three types of

monomer unitsmonomer units

– a nitrogenous base (nucleobases), either purine or a nitrogenous base (nucleobases), either purine or pyrimidine pyrimidine

– a monosaccharide (aldopentose), either D-ribose or 2-a monosaccharide (aldopentose), either D-ribose or 2-deoxy-D-ribosedeoxy-D-ribose

– phosphoric acid/phospharyl groupphosphoric acid/phospharyl group Two types - RNA (Ribonucleic Acid)Two types - RNA (Ribonucleic Acid)

- DNA (Deoxyribonucleic Acid) - DNA (Deoxyribonucleic Acid)

NucleobasesNucleobases Heterocylic compounds containing Heterocylic compounds containing C, H, N, and OC, H, N, and O Purine and pyrimidinePurine and pyrimidine

1 ring structure

2 ring structure

methyl

Nonpolar

(C) (T) (U)

(A) (G)

2 type of aldopentoses found2 type of aldopentoses found

- Ribose (RNA)- Ribose (RNA)

- 2-deoxyribose (DNA)- 2-deoxyribose (DNA) Deoxyribose, derivative of ribose – lacks an Deoxyribose, derivative of ribose – lacks an

oxygen atom at C2oxygen atom at C2

Monosaccharide/sugarMonosaccharide/sugarPolar

Only anomer present in

nucleic acid

NucleosidesNucleosides

Lack phosphate groupLack phosphate group

Pyrimidine Purine

Nucleoside:Nucleoside: a compound that consists of a compound that consists of D-riboseD-ribose or or 2-deoxy-2-deoxy-D-riboseD-ribose (monosaccharide) covalently bonded to a nucleobase (monosaccharide) covalently bonded to a nucleobase by a by a --N-glycosidic bondN-glycosidic bond

Covalent linkage forms between Covalent linkage forms between N9 of purines or N1N9 of purines or N1 of of pyrimidinespyrimidines to to C1 (anomeric carbon of ribose or 2-deoxyribose)C1 (anomeric carbon of ribose or 2-deoxyribose)

NucleotidesNucleotides Nucleotide:Nucleotide: a a nucleoside nucleoside in in

which a molecule of which a molecule of phosphoric phosphoric acid/phosphoryl group acid/phosphoryl group is is esterified with an -OH of the esterified with an -OH of the monosaccharide, at monosaccharide, at the 5’-OHthe 5’-OH

As constituents of cofactors,As constituents of cofactors,

Coenzyme A (CoA), flavin Coenzyme A (CoA), flavin adenine dinucleotide (FAD) & adenine dinucleotide (FAD) & nicotinamide adenine nicotinamide adenine dinucleotides (NAD) dinucleotides (NAD)

Nucleobase, aldopentose sugar and phosphoryl group

Phosphoric acid - polar

5’ = attach to C5 of pentose

SUGAR?

NOMENCLATURE of NOMENCLATURE of NucleotideNucleotide

Based on the nucleoside, plus the phosphate group

Nucleotide SequenceNucleotide Sequence Gene: Sequence of nucleotides that Gene: Sequence of nucleotides that

encodes a polypeptide, eventually encodes a polypeptide, eventually forming a functional proteinforming a functional protein

Gene: a discrete unit of hereditary Gene: a discrete unit of hereditary information consisting of a specific information consisting of a specific nucleotide sequence in DNA (RNA in nucleotide sequence in DNA (RNA in some viruses)some viruses)

The nucleotide sequence is depending on The nucleotide sequence is depending on the bases (nucleobases) present the bases (nucleobases) present

Nucleic Acid:Nucleic Acid:

DNA RNA

1. Bases = ATGC2. Aldopentose =

Ribose3. Phosphoryl group

1. Bases = AUGC2. Aldopentose = Deoxyribose3. Phosphoryl group

Biopolymer, nucleotide as monomer

Naming of nucleotide: if Base adenine Deoxyadenosine 5’ monophosphate

Naming of nucleotide: if Base adenine Adenosine 5’monophosphate

Nucleoside

Nucleic Acid - DNA and RNANucleic Acid - DNA and RNA DNADNA stands for stands for deoxyribonucleic deoxyribonucleic

acidacid. It is the genetic code molecule . It is the genetic code molecule for most organisms.for most organisms.

RNARNA stands for stands for ribonucleic acidribonucleic acid. RNA . RNA molecules are involved in converting molecules are involved in converting the genetic information in DNA into the genetic information in DNA into proteins. In retroviruses, RNA is the proteins. In retroviruses, RNA is the genetic material.genetic material.

NUCLEIC ACIDS ARE POLYMERS OF NUCLEOTIDES

Nucleic Acids DNA or RNA

– consist of a chain of nucleotides joined together by phosphodiester bonds

DNA = material of inheritance, carrier of genetic information

RNA = DNA code is transcribed into RNA which in turn is translated into the corresponding protein

DNAtranscription translation

RNA protein

DNADNA DNADNA and and RNARNA are are polymers polymers

whose monomer unitswhose monomer units are are nucleotides = nucleotides = polynucleotidespolynucleotides

Deoxyribonucleic acids, Deoxyribonucleic acids, DNA:DNA: a biopolymer that a biopolymer that consists of a backbone of consists of a backbone of alternating units of 2-alternating units of 2-deoxy-D-ribose and deoxy-D-ribose and phosphoryl group phosphoryl group

– the 3’-OH of one the 3’-OH of one nucleotide is joined to nucleotide is joined to the 5’ P of the next the 5’ P of the next nucleotide by a nucleotide by a phosphodiester bondphosphodiester bond

Polynucleotide = DNA and RNA

3’ 5’ -phosphodiester bond3’ 5’ -phosphodiester bond

Hydrolysis – break bond

Condensation – form bond

DNA structureDNA structure Levels of structureLevels of structure

– 1° structure1° structure: the order of bases on the : the order of bases on the polynucleotide sequence; the order of polynucleotide sequence; the order of bases specifies the genetic codebases specifies the genetic code

– 2° structure2° structure: the three-dimensional : the three-dimensional conformation of the polynucleotide conformation of the polynucleotide backbone = backbone = double helix structuredouble helix structure

– 3° structure3° structure: supercoiling: supercoiling– 4° structure4° structure: interaction between DNA : interaction between DNA

and proteinsand proteins

DNA - 1° StructureDNA - 1° Structure Primary StructurePrimary Structure:: the the

sequence of bases along sequence of bases along the pentose-the pentose-phosphodiester backbone phosphodiester backbone of a DNA molecule of a DNA molecule – base sequence is read base sequence is read

from the 5’ end to the from the 5’ end to the 3’ end3’ end

– System of notation System of notation single letter (single letter (A,G,C A,G,C and Tand T))

5’ – G G C A T T G C G C - 3’5’ – G G C A T T G C G C - 3’On the right

3’ 5’ -phosphodiester bond3’ 5’ -phosphodiester bond

Pg 237, Campbell and Farrel. READ!

Segment of DNA ChainSegment of DNA Chain

NCCH

C

N

NC

C

N

O

NH2-2

O3POO

CH2

H

O

H

H

HH

NC CH

N

O

CC

O

CH3

O P

O

OO

CH2

H

O

H

H

HH

NC CH

N

O

CHC

NH2

O P

O

OO

CH2

H

OH

H

H

HH

5’-end

3’-end

guanine

thymine

cytosine3’-5’link

• 5’ end – phosphate group is free

• 3’end – 3’ OH in deoxyribose is free

DNA - 2° StructureDNA - 2° Structure Secondary structureSecondary structure:: the ordered the ordered

arrangement of nucleic acid arrangement of nucleic acid strandsstrands

Double helix:Double helix: a type of 2° a type of 2° structure of DNA molecules in structure of DNA molecules in which which two antiparallel two antiparallel polynucleotide strandspolynucleotide strands are coiledare coiled in a right-handed manner about in a right-handed manner about the same axis the same axis

• The chains run The chains run antiparallelantiparallel and are and are held together by hydrogen held together by hydrogen bondingbonding between between complementary complementary base pairsbase pairs: A=T, G=C.: A=T, G=C.

DNA double helix

DNA structural elementsDNA structural elementsOH P

2 right-handed, helical, polynucleotide chains2 right-handed, helical, polynucleotide chains, , coiled around a common axis to form a double helixcoiled around a common axis to form a double helix

2 characteristic: 2 characteristic: Major groove and minor groove Major groove and minor groove – – binding site for drug or polypeptidebinding site for drug or polypeptide

2 strands run in opposite direction 2 strands run in opposite direction

(antiparallel)(antiparallel)-3’,5’-phosphodiester bridges run in -3’,5’-phosphodiester bridges run in opposite directionopposite direction

1 base (purine) 1 base (purine) from single strand link tofrom single strand link to

1 base (pyrimidine) 1 base (pyrimidine) from other stand from other stand (complimentary) (complimentary)

BasesBases are are perpendicularperpendicular to helix to helix axisaxis Polarity and non-polarity regions Polarity and non-polarity regions Aqueous environment – polar, charged, covalent Aqueous environment – polar, charged, covalent

backbone deoxyribose and phosphate groups backbone deoxyribose and phosphate groups outside of the helixoutside of the helix

Hydrophobic purine and pyrimidine bases avoid Hydrophobic purine and pyrimidine bases avoid water by turning towards the inside of the structurewater by turning towards the inside of the structure

Groovy DNA

DNA-protein interaction

T-A Base PairingT-A Base Pairing Base pairing is complementary: Base pairing is complementary: A=T, GA=T, GCC

A major factor stabilizing the double helix is base A major factor stabilizing the double helix is base pairing by hydrogen bonding between T-A and pairing by hydrogen bonding between T-A and between C-Gbetween C-G

T-A base pairT-A base pair comprised of comprised of 22 hydrogen bondshydrogen bonds

Complementary base pairing

G-C Base PairG-C Base Pair

G-C base pair comprised of 3 hydrogen bondsG-C base pair comprised of 3 hydrogen bonds

G-C base pairG-C base pair comprised of 3 comprised of 3 hydrogen bondshydrogen bonds

Forms of DNAForms of DNA B-DNA B-DNA

– considered the considered the physiological formphysiological form– a right-handed helix, inside diameter 11Åa right-handed helix, inside diameter 11Å– 10 base pairs per turn (34Å) of the helix10 base pairs per turn (34Å) of the helix

A-DNAA-DNA– a right-handed helix, but thicker than B-DNAa right-handed helix, but thicker than B-DNA– 11 base pairs per turn of the helix11 base pairs per turn of the helix– has not been found has not been found in vivoin vivo

Z-DNAZ-DNA• a left-handed double helixa left-handed double helix• may play a role in gene expressionmay play a role in gene expression

• Z-DNA occurs in nature, usually consists of Z-DNA occurs in nature, usually consists of alternating purine-pyrimidine basesalternating purine-pyrimidine bases

• Methylated cytosine found also in Z-DNAMethylated cytosine found also in Z-DNA

Structural features of A-, B-, and Z- DNA

Type A-DNA B-DNA Z-DNAHelical senses right handed right handed left handedDiameter (Å) ~26 ~20 ~18Base pairs/turn 11 10 12Major groove narrow/deep wide/deep FlatMinor groove wide/shallow narrow/deep narrow/deep

Pg 294, Concepts in Biochemistry. 3/e 2006 John Wiley & Sons

20 Å

DNA - 3° StructureDNA - 3° Structure Tertiary structure:Tertiary structure: the the

three-dimensional three-dimensional arrangement of all atoms arrangement of all atoms of a nucleic acid; of a nucleic acid; commonly referred to as commonly referred to as supercoilingsupercoiling

Supercoiling-Supercoiling- Further Further coiling and twisting of coiling and twisting of DNA helix.DNA helix.

DNADNA DNA can forms tertiary structure by twist DNA can forms tertiary structure by twist

into complex arrangement – supercoilinto complex arrangement – supercoil Circular DNA:Circular DNA: a type of double-stranded a type of double-stranded

DNA in which the 5’ and 3’ ends of each DNA in which the 5’ and 3’ ends of each strand (2 polynucleotide chains) are strand (2 polynucleotide chains) are joined by phosphodiester bondsjoined by phosphodiester bonds

Can be found in Can be found in microorganisms microorganisms (bacteriophages, bacteria)(bacteriophages, bacteria)

Circular twisted into supercoiled Circular twisted into supercoiled

DNA - DNA - 3° Structure3° Structure Supercoil - results of extra Supercoil - results of extra

twisting in the linear duplex form twisting in the linear duplex form

DNA DNA Circular DNA:Circular DNA: In microorganisms In microorganisms

(bacteriophages, bacteria)(bacteriophages, bacteria)

Circular twisted into supercoiled Circular twisted into supercoiled DNA - DNA - 3° Structure3° Structure

In In eukaryoteseukaryotes, the 3° structure , the 3° structure involves histone (protein)- involves histone (protein)- Chromatin:Chromatin: DNA molecules DNA molecules wound around particles of wound around particles of histones in a beadlike structure histones in a beadlike structure

PROPERTIES OF PROPERTIES OF SUPERCOILSUPERCOIL

Supercoiled is less stable than the relaxed Supercoiled is less stable than the relaxed formform

Compact hence it more easily stored in the Compact hence it more easily stored in the cellcell

Play a regulatory role in DNA replicationPlay a regulatory role in DNA replication

Bacteriophage :

DNA – threadlike structure

Super DNA Coiled TopologySuper DNA Coiled Topology Double helix can be considered to a 2-stranded, Double helix can be considered to a 2-stranded,

right handed coiled roperight handed coiled rope Can undergo positive/negative supercoilingCan undergo positive/negative supercoiling

clockwise

Counterclockwise

DNA - 4° StructureDNA - 4° Structure Four stranded form of DNA (quadruplex DNA)Four stranded form of DNA (quadruplex DNA) Role in regulating and stabilizing telomeres and in Role in regulating and stabilizing telomeres and in

regulation of gene expressionregulation of gene expression Small molecules such as porphyrins and Small molecules such as porphyrins and

anthraquinones present, to stabilize the structureanthraquinones present, to stabilize the structure

G-quadruplex