Lecture 3 DNA RNA Gen Structure Ade FKUI 2012

Lecture 3Nucleic acid and Gene Structure

Biomolecules

Many biomolecules are synthesized from smallermolecules. Such molecules are called polymers.

They include:• DNA and RNA both polymers of nucleotides• Proteins are polymers of amino acids• Polysaccharides are polymers of sugars.

Polymers and Monomers

monomer polymercategory of

biomolecules

monosaccharides polysaccharides carbohydrates

amino acids polypeptides proteins

nucleotides polynucleic acids RNA & DNA

Hyd

roly

sis–

Pol

ymer

Bre

akdo

wn

+ Energy

Enzymes are employed in biological systems to effect most hydrolysis reactions

R

D

In 1860, F. Meischer a Swiss physician isolated a precipitate substance obtained by treatment of white blood cells nuclei, with alkaline solution. The chemical analysis has showed that this precipitate contained Carbon, Nitrogen, Hydrogen, Oxygen and Phosphorus. Meischer called this substance Nuclein.

In 1930 A. Kossel and P. Levene proved that Nuclein was a deoxyribonucleic acid.

In the late 1940's, E. Chargaff discovered the "equimolarity" of bases ([A]=[T], [G]=[C]) and established the coefficient of specificity ((G+C)/(A+T)), which characterise each DNA molecule.

In 1952, Hershey & Chase demonstrated that DNA molecules are the universal support of heridity.

In 1953 J. Watson & S. Crick determined the double helix structure of DNA, owing to the important Xray diffraction works made by R. Franklin. In 1962 Watson, Crick & M. Wilkins were awarded the Nobel Prize for their discovery.

Nitrogen Bases

The nitrogen bases in nucleic acids consist of the:

• Pyrimidines: C U T

• purines : G A

CHCH

Uracil (in RNA)U

CN

NC

OH

NH2

CHCH

OC

NH

CH

HNC

O

CCH3

N

HNC

C

HO

O

CytosineC

Thymine (in DNA)T

NHC

N C

CN

C

CH

N

NH2 O

NHC

NHH

C

C

C

N

NH

C NH2

AdenineA

GuanineG

Purines

Nitrogenous bases Pyrimidines

Pentose Sugars

The pentose (five-carbon) sugar:• In RNA is ribose.• In DNA is deoxyribose. • Has carbon atoms numbered with primes to

distinguish them from the nitrogen bases.

HO

Nucleosides

A nucleoside: • Has a nitrogen base

linked by a glycosidic bond to C1’ of a ribose or deoxyribose.

• Is named by changing the nitrogen base ending to -osine for purines and –idine for pyrimidines

N Base

N-glycosidic linkage

HO

Adenin

DeoxyriboseDeoxyadenosine

NUCLEOSIDE

OHH

glycosidic bond

phosphoester bond

Nucleoside

Names of Nucleosides and Nucleotides

sugar base sugar base phosphate

AMP, ADP, and ATP

• Adding phosphate groups to AMP forms the diphosphate ADP and the triphosphate ATP.

TTT RNARNADNAPURINES TT T

PIRIMIDINES

Primary Structure of Nucleic Acids

DNA Secondary structure

sugar - phosphate

Sugar – phosphate bone causes each DNA chain to coil around the outside of the attached bases

DNA Tertiary structureHydrogen bonding occurs between purines and pirimidines. This causes two DNA strands to bond together. Resulted in a double helix structure.

pentose

pentose

pentose

pentose

The DNA double helix

Nucleotide sequence specifies the amino acid sequence of

proteins

Space-filling model

The double helix structure is mainly stabilized by hydrogen bonds between bases pairs. Since the hydrophobic bases are stacked inside and the hydrophilic ribose-phosphate chains are on the outside, Van der Waals forces and hydrophobic interactions are also deeply involved in the stabilization of the double helix.

In this major or minor grooves, the bases are exposed to solvent and to other molecules. By this way, some chemical and biochemical substances may have interactions with specific bases without disrupting the double helix structure.

Chemicals interaction

Packaging In Prokaryotic cells (cells without nucleus), the two ends of the DNA molecule are joined to form a circular DNA. The circular DNA is coiled into a super helix and often organized in a compact structure containing various proteins and RNAs, named Nucleoid,

In Eukariotic cells, the DNA is packaged in Chromatin within the nucleus. The structure of chromatin is determined and stabilized through the interaction of the DNA with specific bindings proteins.

Considering that human cell nucleus has a diameter of only 10 micrometers, whereas total DNA (genome) contained 46 chromosome, about 3x109 base pairs, and a length 1 m if streched end to end, so that DNA duplex must be highly compacted to fit into the nucleus.

This compaction is achieved by the double helix being folded around structure called nucleosome core. Each nucleosome is composed of 8 different protein called histones. The DNA duplex wraps around the nucleosome core to form a chain of nucleosome (about 150 – 200 base pairs per nucleosome).

An external ninth histone (H1 linker histone) is added which holds the nucleosome structure together. A nucleosome plus one H1-histone is termed a chromatosome.With the aid of histones H1, nucleosomes may be packed together and wound into a regular coil called solenoid. A solenoid contains six to eight nucleosomes per turn and forms the 30nm nucleoprotein fibers or chromatin fiber.

= holds the nucleosome structure together

Chromatosome

H1 histone

nucleosome

20 – 200 nucleotides pairs

20 – 200 nucleotides pairs

20 – 200 nucleotides pairs

H1 histone

Tetrameric molecules: H2A, H2B, H3 and H4( 4 histone-subunits )

The DNA helix coils twice around the histone octamer

How DNA can be bound to the nucleosome core ?NH3

+ PO4-3

Nucleosomes are separated one another by a linker segments of 20-200 nucleotides pairs. This gives unfolded chromatin a "beads-on-a-string" appearance.

DNA Denaturation

1.Temperature

random coil conformation

2.Hyperchromiceffect

Increasing in UV absorbance

decrease interaction between bases

RNA

To form RNA polymer, the ribonucleotide units are connected by a phosphodiester bond between the 3’ hydroxyl group (-OH) of one ribonucleotide and the 5’ hydroxyl group of another ribonucleotide.

RNA types• transfer RNA (tRNA)• messenger RNA (mRNA)• ribosomal RNA (rRNA)• small interfering RNA (siRNA)• micro RNA (miRNA)• small nucleolar RNA (snoRNA)

RNA Base Pairing tRNA

Genes• Genes are the basic physical and functional units

of heredity. Each gene is located on a particular region of a chromosome and has a specific ordered sequence of nucleotides (the building blocks of DNA).

• The sequence of nitrogen bases along a DNA or mRNA polymer is unique for each gene.

• Genes are normally hundreds to thousands of nucleotides long.

What is a locus?• A locus describes the region of

a chromosome where a gene is located. 11p15.5 is the locus for the human insulin gene. 11 is the chromosome number, p indicates the short arm of the chromosome, and 15.5 is the number assigned to a particular region on a chromosome. When chromosomes are stained in the lab, light and dark bands appear, and each band is numbered. The higher the number, the farther away the band is from the centromere.

Exons vs Introns• Eukaryotic genes have introns and exons.

Exons contain nucleotides that are translated into amino acids of proteins. Exons are separated from one another by intervening segments of junk DNA called introns. Introns do not code for protein. They are removed when eukaryotic mRNA is processed. Exons make up those segments of mRNA that are spliced back together after the introns are removed; the intron-free mRNA is used as a template to make proteins.

Splicing• Exons are sequences of DNA that are

expressed into protein.• Introns are intervening sequences that are not

translated into protein

DNA

Pre-mRNA

31

1 2 3

1 32

2Spliced mRNA

3

C

C

C

• The flow of genetic information is from DNA -> RNA -> protein.– Protein synthesis occurs

in cellular structurescalled ribosomes.

– In eukaryotes, DNA is located in the nucleus, but most ribosomes are in the cytoplasm with mRNA as an intermediary.

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 5.28

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