Chemical structure of nucleosides and nucleotides and their nomenclature

Gihan E-H Gawish, MSc, PhDAss. Professor

Molecular Genetics and Clinical Biochemistry

KSU

T H I R D W E E K

KNOW THE STRUCTURES AND

NOMENCLATURE OF THE BUILDING BLOCKS

OF NUCLEIC ACIDS

• P U R I N E A N D P Y R I M I D I N E

• B A S E S N U C L E O S I D E N U C L E O T I D E S

• R I B O N U C L E O T I D E S A N D D E O X Y R I B O N U C L E O T I D E S

Learning objectives:

Three components

1. Pentose (5-carbon) sugar

DNA = deoxyribose

RNA = ribose

(compare 2’ carbons)

2. Nitrogenous base

Purines

Adenine

Guanine

Pyrimidines

Cytosine

Thymine (DNA)

Uracil (RNA)

3. Phosphate group attached to 5’ carbon

Nucleotide = monomers that make up DNA and RNA

A base + a sugar is a

nucleosid

nucleoside + phosphate

is a nucleotide

(nucleotides named by

nucleoside plus number

of phosphates –

adenosine diphosphate)

Nitrogen on C-1’ position

Phosphate commonly on

C-5’

Nucleosides and Nucleotides

Portion of polynucleotide chain of deoxyribonucleic acid (DNA). The inset shows the corresponding pentose sugar and pyrimidine base in ribonucleic acid (RNA).

DNA structure, showing the nucleotide bases cytosine (C), thymine (T), adenine (A), and

guanine (G) linked to a backbone of alternating phosphate (P) and deoxyribose sugar (S)

groups. Two sugar-phosphate chains are paired through hydrogen bonds between A and T

and between G and C, thus forming the twin-stranded double helix

Animation

Phosphodiester Bonds

Covalent bond between the phosphate group (attached to 5’ carbon) of one nucleotide and the 3’ carbon of the sugar of another nucleotide.

This bond is very strong, and for this reason DNA is remarkably stable.

DNA can be boiled and even autoclaved without degrading

5’ and 3’

The ends of the DNA or RNA chain are not the same.

One end of the chain has a 5’ carbon and the other end has a 3’ carbon.

Nucleotides are linked by phosphodiester bonds to form polynucleotides

5’ end

3’ end

James D. Watson & Francis H. Crick - 1953

Double Helix Model of DNA

Two sources of information:

1. Base composition studies of Erwin Chargaff

• indicated double-stranded DNA consists of ~50% purines (A,G) and ~50% pyrimidines (T, C)

• amount of A = amount of T and amount of G = amount of C(Chargraff’s rules)

• %GC content varies from organism to organism

Examples: %A %T %G %C %GC

Homo sapiens 31.0 31.5 19.1 18.4 37.5Zea mays 25.6 25.3 24.5 24.6 49.1Drosophila 27.3 27.6 22.5 22.5 45.0Aythya americana 25.8 25.8 24.2 24.2 48.4

James D. Watson & Francis H. Crick - 1953

Double Helix Model of DNA

Two sources of information:

2. X-ray diffraction studies - Rosalind Franklin & Maurice Wilkins

Conclusion-DNA is a helical structure with distinctive regularities, 0.34 nm & 3.4 nm.Fig. 2.12

Double Helix Model of DNA: Six main features

1. Two polynucleotide chains wound in a right-handed (clockwise) double-helix.

2. Nucleotide chains are anti-parallel: 5’ 3’ 3’ 5’

3. Sugar-phosphate backbones are on the outside of the double helix, and the bases are oriented towards the central axis.

4. Complementary base pairs from opposite strands are bound together by weak hydrogen bonds.

A pairs with T (2 H-bonds), and G pairs with C (3 H-bonds).

e.g., 5’-TATTCCGA-3’3’-ATAAGGCT-3’

5. Base pairs are 0.34 nm apart. One complete turn of the helix requires 3.4 nm (10 bases/turn).

6. Sugar-phosphate backbones are not equally-spaced, resulting in major and minor grooves.

Animation

1962: Nobel Prize in Physiology and Medicine

James D.Watson

Francis H.Crick

Maurice H. F.Wilkins

What about?Rosalind Franklin

Yeast Alanine tRNA

RNA (A pairs with U and C pairs with G)

Examples:mRNA messenger RNAtRNA transfer RNArRNA ribosomal RNAsnRNA small nuclear RNA

RNA secondary structure:

single-strandedFunction in transcription(RNA processing) and translation

Organization of DNA/RNA in chromosomes

Genome = chromosome or set of chromosomes that contains all the DNA of an organism (or organelle) possesses

Viral chromosomes 1. single or double-stranded DNA or RNA2. circular or linear3. surrounded by proteins

TMV T2 bacteriophage bacteriophage

Prokaryotic chromosomes

1. most contain one double-stranded circular DNA chromosome2. others consist of one or more chromosomes and are either circular or linear3. typically arranged in a dense clump in a region called the nucleoid

Problem:

Measured linearly, the Escherichia coli genome (4.6 Mb) would be 1,000 times longer than the E. coli cell.

The human genome (3.4 Gb) would be 2.3 m long if stretched linearly.

Solutions:

1. Supercoiling DNA double helix is twisted in space about its own axis, a process is controlled by topoisomerases (enzymes). (occurs in circular and linear DNA molecules)

2. Looped domains

Fig. 2.22

More about genome size:

C value= total amount of DNA in the haploid (1N) genome

Varies widely from species to species and shows no relationship to structural or organizational complexity.

Examples C value (bp)

48,502T4 168,900HIV-1 9,750E. Coli 4,639,221Lilium formosanum 36,000,000,000Zea mays 5,000,000,000Amoeba proteus 290,000,000,000Drosophila melanogaster 180,000,000Mus musculus 3,454,200,000Canis familiaris 3,355,500,000Equus caballus 3,311,000,000Homo sapiens 3,400,000,000

Eukaryotic chromosome structure

Chromatin complex of DNA and chomosomal proteins~ twice as much protein as DNA

Two major types of proteins:

1. Histones abundant, basic proteins with a positive chargethat bind to DNA

5 main types: H1, H2A, H2B, H3, H4

~equal in mass to DNA

evolutionarily conserved

2. Non-histones all the other proteins associated with DNA

differ markedly in type and structure

amounts vary widely>> 100% DNA mass<< 50% DNA mass

Packing of DNA into chromosomes:

1. Level 1 Winding of DNA around histones to create a nucleosome structure.

2. Level 2 Nucleosomes connected by strands of linker DNA like beads on a string.

3. Level 3 Packaging of nucleosomes into30-nm chromatin fiber.

4. Level 4 Formation of looped domains.

More about different types of DNA you should know about:

•Centromeric DNA (CEN) Center of chromosome, specialized sequences function with the microtubles and spindle apparatus during mitosis/meiosis.

•Telomeric DNA At extreme ends of the chromosome, maintain stability, and consist of tandem repeats. Play a role in DNA replication and stability of DNA.

Repeated DNA:

•Unique-sequence DNA Often referred to as single-copy and usually code for genes.

•Repetitive-sequence DNA May be interspersed or clustered and vary in size.

SINEs short interspersed repeated sequences (100-500 bp)

LINEs long interspersed repeated sequences (>5,000 bp)

Microsatellites short tandem repeats (e.g., TTA|TTA|TTA)

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ggawish@ksu.edu.sa