Nucleic Acid Structure

Biomedical importance of nucleic acids:chemical basis for heredity

• A nineteenth-century monk called Gregor Mendel introduced the notion of genes: basic units responsible for possession and passing on of a single characteristic (eg. colour of hair)

• Initially it was thought that proteins carried genetic information, until mid 20th-century, when it was found that DNA did.

• Proteins are the functional molecules in cells (ie. they perform the majority of the reactions necessary to life)

Nucleic acids are DNA and RNA

DNA• The principal location of DNA is the

nucleus of eukaryotic cells.• Secondary locations of DNA are

mitochondria.

RNA• The different types of RNA are located in

nucleus, cytoplasm, mitochondria, ribosomes.

The Central Dogma

RNA

Protein

DNA

Proposed by Francis Crick in 1958 to describe the flow of information in a cell.

Information stored in DNA is transferred residue-by-residue to RNA which in turn transfers the information residue-by-residue to protein.

The Central Dogma proposed by Crick has undergone numerous revisions in the past 47 years.

deoxyribonucleic acid

ribonucleic acid

The Central Dogma• DNA RNA protein

Transcription Translation• transcription = transfer of genetic information

from DNA to RNA • translation = transfer of genetic information from

RNA to functional protein molecules, in which the amino acid sequence is encoded in the structure of the DNA.

• replication = transfer of genetic information from mother-cell to daugther-cells through synthesis of a two identical copies of DNA

Revision of Central Dogma• Recombination =

rearrangements of genes

• Mutation/Repair = damage to DNA which altered the genetic information/ correction of damaged DNA

• Reverse transcription = transfer of genetic information from RNA to DNA

Recombination

Mutation/Repair

What are nucleic acids (DNA and RNA)?

• Nucleic acids are poly-nucleotides.

• The monomeric units of nucleic acids are nucleotides, which are composed of:

- a heterocyclic nitrogenous base: - purines: adenine (A) and guanine (G)- pyrimidines: cytosine (C) and thymine (T) for

DNA cytosine (C) and uracyl (U) for

RNA- a sugar:

- deoxyribose (is present in DNA)- ribose (is present in RNA)

- phospate

STRUCTURE OF NITROGENOUS BASES

Pyrimidines

• The atoms of the pyrimidines are given numbers from 1 to 6.

N

NH

NH2

ONH

NH

O

O

CH3

NH

NH

O

O

C ytos ine Thym ine U rac il

1

2

3

4

5

6

Purines

A den ine

N

N

NH

N

NH2

N

NH

NH

N

NH2

O

G uan ine

1 2

3

4

5

6 7

8

9

• The atoms of purines are given numbers from 1 to 9.

STRUCTURE OF SUGAR MOIETIES FROM NUCLEIC

ACIDS

What are nucleic acids (DNA and RNA)?

• Nucleic acids are poly-nucleotides.

• The monomeric units of nucleic acids are nucleotides, which are composed of:

- a heterocyclic nitrogenous base: - purines: adenine (A) and guanine (G)- pyrimidines: cytosine (C) and thymine (T) for

DNA cytosine (C) and uracyl (U) for

RNA- a sugar:

- deoxyribose (is present in DNA)- ribose (is present in RNA)

- phospate

Sugars

• The carbons of the sugar are given numbers from 1’ to 5’.• The sugar of DNA is deoxyribose, which lacks 2’-OH.• The sugar of RNA is ribose.

OHO

CH2OH

OHOH

OHO

CH2OH

OH

R ibose D eoxyribose

1’2’3’

4’

5’

lacks 2’-OH

STRUCTURE OF NUCLEOSIDES

Structure of nucleosides: base + sugar

• Nucleosides are derivatives of purines and pyrimidines that have sugar linked to a ring nitrogen:N9 for purinesN1 for pyrimidines

via a β-N-glycosidic bond.

β-N-glycosidic bond

STRUCTURE OF NUCLEOTIDES

Structure of nucleotides• Nucleotides are composed of nucleosides (base + sugar) and 1, 2, or 3

groups of phosphate. • Mononucleotide (nucleoside-monophosphate)= nucleoside + 1 phosphate• Nucleoside-diphosphate = nucleoside + 2 phosphates• Nucleoside-triphosphate = nucleoside + 3 phosphates

Quick Quiz Question

• The following statements are correct:

1. Nucleosides consists of a sugar, a nitrogenous base and phosphate.

2. The sugar found in DNA is represented by deoxyribose.

3. Cytosine and thymine are purines.

4. DNA is located in nucleus and mitochondria.

Ribonucleosides/RibonucleotidesTerminology(where sugar = ribose)

Base Nucleoside Nucleotide

Adenine (A)

Adenosine (A)=Adenylate

Adenosine monophosphate (AMP)

Adenosine diphosphate (ADP)

Adenosine triphophate (ATP)

Ribonucleosides/RibonucleotidesTerminology(where sugar = ribose)

Base Nucleoside Nucleotide

Adenine (A) Adenosine (A)=Adenylate

Adenosine monophosphate (AMP)Adenosine diphosphate (ADP)Adenosine triphosphate (ATP)

Guanine (G) Guanosine (G)=Guanylate

Guanosine monophosphate (GMP)Guanosine diphosphate (GDP)Guanosine triphosphate (GTP)

Cytosine (C) Cytidine (C)= Cytidylate

Cytidine monophosphate (CMP)Cytidine diphosphate (CDP)Cytidine triphosphate (CTP)

Uracil (U) Uridine (U)=Uridylate

Uridine monophosphate (UMP)Uridine diphosphate (UDP)Uridine triphosphate (UTP)

Thymine (T) Thymidine (T)=Thymidylate

Thymidine monophosphate (TMP)Thymidine diphosphate (TDP)Thymidine triphosphate (TTP)

Comparative terminology

• Ribonucleotides Deoxyribonucleotides

Adenosine monophosphate (AMP)

Deoxyadenosine monophosphate (dAMP)

Adenosine diphosphate (ADP)

Deoxyadenosine diphosphate (dADP)

Adenosine triphosphate (ATP)

Deoxyadenosine triphophate (dATP)

DeoxyNucleosides/DeoxyNucleotidesTerminologywhere sugar = deoxyribose

Base Nucleoside Nucleotide

Adenine (A) Deoxyadenosine (A)=Deoxyadenylate

Deoxyadenosine monophosphate (dAMP)Deoxyadenosine diphosphate (dADP)Deoxyadenosine triphophate (dATP)

Guanine (G) Deoxyguanosine (G)=Deoxyguanylate

Deoxyguanosine monophosphate (dGMP)Deoxyguanosine diphosphate (dGDP)Deoxyguanosine triphophate (dGTP)

Cytosine (C) Deoxycytidine (C)=Deoxycytydylate

Deoxycytidine monophosphate (dCMP)Deoxycytidine diphosphate (dCDP)Deoxycytidine triphophate (dCTP)

Uracil (U) Deoxyuridine (U)=Deoxyurydylate

Deoxyuridine monophosphate (dUMP)Deoxyuridine diphosphate (dUDP)Deoxyuridine triphophate (dUTP)

Thymine (T) Deoxythymidine (T)=Deoxythymidylate

Deoxythymidine monophosphate (dTMP)Deoxythymidine diphosphate (dTDP)Deoxythymidine triphophate (dTTP)

Physiological functions of nucleotides

• “Bricks” for nucleic acids synthesis • Macroergic compounds which deliver energy

necessary to different biological processes (eg. ATP, GTP)

• Allosteric regulators of different enzymes• Methyl group donor (eg. S-adenosylmethionine)• Signal transduction: intracellular messengers of

hormones (eg. AMPc, GMCc)

Free natural nucleotides: cAMP

OCH2

OP

O

O

A den ine

N

N

N

N

NH2

O

OH

R ibose

AMPc

• 3’,5’cyclic adenosine monophosphate (cAMP) serves as a second messenger or transducer of information between the extracellular and intracellular medium.

Classification of nucleotides

• Mononucleotides= monomeric unit • Oligonucleotides= contain 2-10 monomeric

units (nucleotides) joined together by 3’5’ phosphodiester bridges/bonds

• Polynucleotydes= contains more than 10 monomeric units.

STRUCTURE OF DNA

1. primary structure2. secondary structure

3. tertiary structure

PRIMARY STRUCTURE OF DNA

James Watson Francis Crick

1962 Nobel Prize

http://www.sciencemag.org/cgi/content/full/300/5617/255http://www.lecb.ncifcrf.gov/~toms/icons/Watson.Crick.Nature.jpg

Polynucletide chain of DNA(primary/covalent structure)

N

NH

N

N

NH2

O G uan ine

OCH2OH

O

OCH2

O

PO

O

O

PO O

O

N

N

NH2

O

C ytos ine

OCH2

OH

PO

O

O

NH

NH

O

O

CH3

Thym ine

3' end

5' end

• The polynucleotide chain of DNA consist of nucleotides joined together by 3’,5’ phosphodiester bonds.

• Phosphodiester bonds link the 3’- and 5’-sugar carbons of adiacent monomer.

• Polynucleotides are directional macromolecules: each end of a polymer is distinct.

• 3’ –end is one with a free 3’-hydroxyl.

• 5’ –end is one with a free or phosphorilated 5’-hydroxyl.

• Polynucleotides bear a negative charge at physiological pH

3’linkage

5’linkage

1’

N

NH

N

N

NH2

O G uan ine

OCH2OH

O

OCH2

O

PO

O

O

PO O

O

N

N

NH2

O

C ytos ine

OCH2

OH

PO

O

O

NH

NH

O

O

CH3

Thym ine

3' end

5' end

P

P

P

G

C

T

OH

OH

Simplified representation of DNA chain

5’

5’

5’

3’

3’

3’

Sugar: horisontal line

Base: single letter

Phosphodiester bond:

oblique line with P

N

NH

N

N

NH2

O G uan ine

OCH2OH

O

OCH2

O

PO

O

O

PO O

O

N

N

NH2

O

C ytos ine

OCH2

OH

PO

O

O

NH

NH

O

O

CH3

Thym ine

3' end

5' end

Simplified representation of DNA chain

Convention dictates that a single-stranded DNA sequence is written in the 5’ to 3’ direction.

e.g. GCT means 5’GCT 3’

Quick Quiz

Question :

• Identify which is the 3’end of this oligonucleotide?

• Write the simplified representation of this oligonucleotide.

SECONDARY STRUCTURE OF DNA

Double helix of DNA

• Watson and Crick discovered the secondary structure of DNA: a double helix – two sugar phosphate chains wrapping round each other, with the phosphate groups sticking out – the nucleotide from strand 1 meets the nucleotide from strand 2 in the middle. These pairs of nucleotides are complementary – where one strand has a C, the other has a G and vice versa; where one strand has an A the other has a T and vice versa.

• Human DNA consists of approximately 3 x 109 such “base pairs”.

1. DNA is double stranded: each molecule of DNA is composed of two polynucleotide chain that are joined together by formation of hydrogen bonds between the bases.

2. DNA strands are twisted to form a double helix.

3. DNA strands are antiparallel (one strand runs in the 5’ to 3’ direction and the other in the 3’ to 5’ direction, analogous to two street lanes carrying traffic in opposite direction).

The DNA double helix(secondary structure)

3. G-C pairs have 3 hydrogen bonds

A-T pairs have 2 hydrogen bonds

4. One strand is the complement of the other, as they are formed by complementary bases (G is complementary to C, while A is complementary to T).

5. The concentration of deoxyadenosine (A) nucleotides equals that of thymidine (T) nucleotides (A=T), while the concentration of deoxyguanosine (G) nucleotides equals that of deoxycytidine (C) nucleotides (G=C)

The DNA double helix(secondary structure)

Quick Quiz Question

1. Writte the complementary strand of the following DNA strand: ATTTTAAGCTAAGGCCCTTT

2. Calculate the number of the hydrogen bonds existing beteen the complementary strands

3. Specify which base is at the 3’end of this strand and which base is at the 3’ end of its complementary strand.

6. The B form of DNA described by Watson and Crick is right handed.

7. The distance spanned by one complete turn of the B-DNA double helix is 34 Å.

8. One turn of B-DNA includes 10 base pairs.

9. Oter forms of DNA include:- A-DNA which is more compact than B-DNA- Z-DNA is left handed and its bases are positioned more toward the periphery of the helix.

The DNA double helix(secondary structure)

Quick Quiz Question

• DNA1. Is composed of nucleosides joined by

phosphodiester bonds2. Contains negatively charged phosphate groups3. Contains base pairs A/T and G/C4. Consists of two strands which run in the same

direction.

What are the hydrogen bonds inside the DNA double helix?

• Hydrogen bonds represent non-covalent (relatively weak) intermolecular bonds which are caused by the polarity of H-O bond.

“TERTIARY” STRUCTURE OF DNA:

the polynucleosome

From DNA to Chromosomes

• In eukaryotes, the DNA is stored in the nucleus. Since there is not much space and DNA molecules are extremely large (the length of DNA from one singlehuman cell is 2m!!!), the DNA must be highly organised.

• There are five levels of DNA compaction (or packing) that result in a 10.000 –fold decrease in DNA length.

Levels of packing of DNA in the nucleus

-the first level-

r• The DNA double helix is

wrapped around protein complexes called histones- each unit of DNA wrapped round a histone complex is called a nucleosome.

• Histones are small proteins, rich in basic aminoacids (Arg, Lys).

Levels of packing of DNA in the nucleus

- the first level-

r • Nucleosome contains an octameric core formed by two molecules of each histones H2A, H2B, H3, H4, around which 140 base pairs of DNA are wrapped.

• The nucleosomes are separated by a small distance (DNA linker formed by 30 base paires). H1 histones interact with DNA linker.

• The polynuceosome structure of DNA are similar to the “beads on a string” (=10nm fibrils of chromatin).

Amethyst Beads on a String

r

“Beads on a string” appearance of DNA

Levels of packing of DNA in the nucleus-the second level-

• The polynucleosome chain is further compacted to form solenoid structures.

• Solenoid structure has 6-7 nucleosomes pe turn.

• Solenoid structure form the 30 nm fiber of chromatin.

r

Levels of packing of DNA in the nucleus-the third, fourth and fifth levels-

r- The chromatin fibres fold together to form large looped domains.

- These looped domains are then supercoiled and organised into distinct structures called chromosomes.

- The human nuclear DNA ( genome) consists of 23 pairs of chromosomes.

The difference between diploid and haploid cells

• Many eukaryotic cells contain pairs of chromosomes and are hence called diploid.

• Other cells contain single chromosomes and are called haploid.

The chromosomes of the human genome

ENOUGH !!!