DNA Structure

By Dr. Walaa Bayoumie El Gazzar

Nucleic acids

• Polymer of nucleotides.

• Two main types:

DNA

RNA

• All cellular functions depend on proteinswhich consist of chains of amino acids.

• The precise arrangement of these amino acids

necessitates certain guiding information.necessitates certain guiding information.

• Such information is provided by DNA which

can convey information through a group of

RNA.

Nucleotides

Phosphate

Nitrogenous

Base

Pentose

Sugar

Nitrogenous

Base

DNA Structure

�DNA consists of two strands ofpolynucleotides.

DNA 1ry structure :DNA 1ry structure :

�The sequence of nucleotides

�The order of nucleotides in any DNA strand is

written in the 5’ to3’ direction

• The nucleotide in each strand covalentlylinked by phosphodiester bonds betweenphosphate at 5’of one nucleotide and 3\

hydroxyl group of deoxyribose of the nextnucleotide.

• Each strand has two ends, 3\ end with freehydroxyl group and 5\ end with free 5\hydroxyl group and 5\ end with free 5\

phosphate group.

• The two DNA strands run antiparalleldirection this means that one strands runfrom 3\to 5\ while the other strand run from5\to 3\.

• The sequence of nucleotide is always read

from 5\ to 3\ direction e.g. 5\pGpApCp 3\ or

GAC.

• The sugar phosphate unites form the

backbone of DNA strand (S-P-S-P) while

nitrogenous bases are projecting to the insidenitrogenous bases are projecting to the inside

in between the two strands.

• The sequence of bases determines the coding

structure of DNA ( genetic information)

DNA 2ry structure :

� Watson and crick proposed a structure for DNA inthe form of a double helix (B form ) which is themost common physiological form. It has thefollowing characters:

1-Two antiparallel strands form a right handedhelix: one runs in the 5’ to3’ direction and theother in the 3’ to 5’ direction. The two strands arepaired to each other & coil around a common axisto form a right handed helix.

• 2-complementary base pairing: The two strandsare held together by hydrogen bonds betweenthe complementary base pairs, adenine formstwo hydrogen bonds with thymine and guanineforms three hydrogen bonds with cytosine. Thusthe number of adenine equals that of thymineand the number of guanine equals that ofcytosine in DNA.

• The sequence of bases in one strand determines• The sequence of bases in one strand determinesthe sequence of the other during DNA replicationto transfer genetic information in a correctmanner as each of the original DNA strand acts asa template for synthesis of a new complementarystrand to form two daughter DNA molecules.

�3- Base stacking: the base pairs are stacked

above each other by van der waals forces and

hydrophobic interactions so stability of the

helix is provided by :

Van der waals forcesVan der waals forces

Hydrophobic interactions

Hydrogen bonding between complementary

base pairs

• Van der waals forces: a class of transient

electrostatic interaction. The attraction between

molecules is greatest at a distance called the Van

der waals distance (0.3 to 0.4 nm). If molecules

approach each other more closely, a repulsive

force develops, by the negative charges of theirforce develops, by the negative charges of their

outer electron shells.

• Hydrophobic interactions: nonpolar molecules

cannot form hydrogen bonds with water

molecules and tend to cluster together and they

are insoluble in water

• 4-Dimensions:-2 nm wide, each complete turn is 3.4 nm long

in which there is 10.4 base pairs.

-Two grooves are apparent from outside, a

major groove (2.2 nm) and a minor groovemajor groove (2.2 nm) and a minor groove

(1.2 nm), through which many drugs or

proteins can make contact with the

nitrogenous bases without any need to open

the helix as in these grooves the bases are

exposed.

Denaturation of DNA

Rupture of hydrogen

bonds and separation of

the two strands

Heating

The temp. that produces loss of 50% of DNA

helical form is termed the melting temp.(Tm)

Cooling of denatured DNA results in reformation

of the double helix or renaturation or

reannealing

• Gene:-It can be defined as a segment of DNA that

code for a polypeptide chain depending onthe sequence of the bases in the DNA.

-Every 3 bases form a code that determines-Every 3 bases form a code that determines

an amino acid.

-The position of a gene along a chromosome iscalled the locus of the gene.

Most eukaryotic genes are discontinuous

contain coding regions (exons or expressed

sequences) and noncoding regions (introns).

• Human genome:-It can be defined as the total DNA content in the

chromosomes of the cell (total geneticinformation presented by the group ofchromosomes in any cell).

- The human genome is the complete set- The human genome is the complete setof nucleic acid sequences for humans, encodedas DNA within the 23 chromosome pairs in cellnuclei and in a small DNA molecule found withinindividual mitochondria.

- Human genomes include both protein-codingDNA genes and noncoding DNA.

• The content of the human genome is commonlydivided into coding and noncoding DNA sequences.

�Coding DNA is defined as those sequences that can betranscribed into mRNA and translated into proteinsduring the human life cycle; these sequences occupyonly a small fraction of the genome (<2%).

� Noncoding DNA is made up of all of those sequences� Noncoding DNA is made up of all of those sequences(98% of the genome) that are not used to encodeproteins.

• Some noncoding DNA contains genes for RNAmolecules with important biological functions(noncoding RNA, for example ribosomalRNA and transfer RNA).

• There are an estimated 19,000-20,000 human

protein-coding genes. The estimate of the

number of human genes has been repeatedly

revised down from initial predictions of

100,000 or more as genome sequence quality

and gene finding methods have improved,

and could continue to drop further.and could continue to drop further.

• Protein-coding sequences account for only a

very small fraction of the genome

(approximately 1.5%)

• Haploid human genomes, which are

contained in germ

cells (the egg and sperm gamete cells) consist

of three billion DNAbase pairs,of three billion DNAbase pairs,

while diploid genomes (found in somatic

cells) have twice the DNA content.

• Genotype : if the two genes (alleles) at certain locusin an individual are indistiguishable from each other,the genotype is homozygous for these genes- if the twogenes are different from each other, the genotype issaid to be heterozygous.( what is on the inside of thegenes in DNA)

• An allele is a variant form of a given gene.

• Phenotype : the physical or biochemical expression• Phenotype : the physical or biochemical expressionof the genotype ( what is the outside or theobservable traits)

• Most complex traits are influenced by many genes andby environment e.g. skin color, hair color, weight,behavior and some diseases like diabetes mellitus. Thismeans that the same genotype can result in differentphenotype depending on the environment.

• Eukaryotic cells: cells that are divided by internalmembranes into subcellular compartments such as thenucleus, mitochondria, and endoplasmic reticulum.

• Prokaryotic cell (e.g. a bacterial cell) is not subdivided byinternal membranes and so characteristically has nodefinite nuclear membrane. Each cell contains one singledouble –stranded supercoiled circular chromosome.

-In addition, most species of bacteria also contain small andcircular extrachromosomal DNA molecules calledplasmids. Plasmid DNA carries genetic information & maycarry genes that convey antibiotic resistance to the hostbacterium.

• Chromatin consists of very long

double-stranded DNA molecules and a nearly

equal mass of small basic proteins termed

histones as well as a smaller amount of non-

histone proteins (most of which are acidic andhistone proteins (most of which are acidic and

larger than histones) and a small quantity of

RNA.

• Non-histone proteins: This class of proteins includes the

various transcriptional factors, polymerases, hormone

receptors and other nuclear enzymes.

DNA Tertiary structure:It is the folding of long DNA molecule to

decrease its size and allow its packing insidedecrease its size and allow its packing inside

the cell this is called (DNA supercoiling)