nucleic acid structure and organization

Nucleic Acid Structure and Organization

Asmarinah

Department of Medical Biology

Nucleic acid

- Macromolecules consisting of a chain of nucleotides joined together by phosphodiester bonds

- divided into:

DNA (Deoxyribonucleic acid) molecules

RNA (Ribonucleic acid) molecules

DNA and its building

DNA is made from subunits, called nucleotides

Each nucleotide consisting of

-Sugar (deoxyribose)

-Phosphate

-Base: Adenine

Thymine

Guanine

Cytosine

DNA - GeneA gene is defined as a segment of DNA that contains the insctruction for making a particular protein

● DNA molecules are organized into chromosome

● Chromosome: A DNA molecule with its attendant proteins that moves as an independent units during mitosis and meiosis

Before DNA replication, each chromosome consists of a single DNA molecule plus protein, is called a chromatid

After replication, each chromosome consists of two identical DNA molecule plus proteins; this are called sister chromatids

● Chromatin: DNA plus the proteins that package it within the cell nucleus

A B C

A. The principal structural features of chromosome

B. An electron micrograph of human mitotic chromosomes

C.A diagram of various classes of human chromosomes

Chromatin packing occurs on several levels

Structural organization of nucleosome

Nucleosome contains

Octameric histon protein & DNA double helix

Genome

The totality of genetic information belonging to a cell or an organism; in particular, the DNA that carries this information

Genomics

The science of studying the DNA sequences and properties of entire genomes

Each human chromosome has a unique banding pattern

Human Genome

The Organization of human genome

Conserved gene order in chromosome between the human (a) and mouse (b) genome

Closely related species can have very different chromosome numbers

Chromosomes from many eucaryotes (including human) contain a large excess of interspersed DNA that does not seem to carry critical information, called junk DNA

This DNA may not be important, but can play a role:

- as spacer material

- for long-term evolution of the species

- for the proper expression of genes

Bacteria and some single-celled eucaryotes have especially compact genomes. The complete nucleotide sequence of their genomes reveals that DNA molecules are little more than strings of closely packed genes

Mitochondrial DNAMitochondrial DNA

Chromosome No. 25Chromosome No. 25 Genome Genome circular double circular double

stranded DNA stranded DNA Maternal inherited Mito DNA : 16.569 bp Mito DNA : 16.569 bp Nuclear DNA : 3 x 10Nuclear DNA : 3 x 1099 bp bp

The structure of mitochondria

- contains two membranes:

* outer mitochondrial membrane

* inner mitochondrial membrane

-There is two aqueous compartment:

* Matrix, within the interior

* Intermembrane space, between

OMM and IMM

produce ATPproduce ATP

5 respiration enzyme complexes5 respiration enzyme complexes

complex I (NADH oxydoreductase : Ubiquinone)complex I (NADH oxydoreductase : Ubiquinone)complex II (suksinat oxydoreductase : ubiquinone)complex II (suksinat oxydoreductase : ubiquinone)complex III (ubiquinol oxydoreductase : sitokrom c)complex III (ubiquinol oxydoreductase : sitokrom c)complex IV (Cytocrome c oxydase)complex IV (Cytocrome c oxydase)complex V (ATPsynthase). complex V (ATPsynthase).

Role of mitochondria

The genome of E. coli

A. E.coli strain K-12 has 4.639.221 nucleotides pairs

B. A diagram of the E. coli genome.

E. Coli genome is circular that forms a single, closed loop.

Yellow or orange bars shows protein-coding genes

Green arrows indicate genes encoding only RNA molecules

Genetic differences between pathogen and nonpathogen bacteria

Example: Genetic organization of Vibrio cholerae

A. Vibrio cholerae has two circular chromosomes, that each of its has distinct origin of replication (oriC1 &

oriC2)

CTXφ locus carriers the gene for cholera toxin

VPI island contains gene for factors required for intestinal colonization

B. Map of CTXφ locus consist of: - core region: gene for cholera toxin ctxA & ctxB

gene for involving of virulence (ace & zot)

- repeated sequence RS2 & RS1 that involved

chromosomal insertion of bacteriophage genome

Schematic drawings of several types of viral genomes

RNA

Polymer formed from covalently linked ribonucleotide monomer

Type of RNA:

-mRNA = messenger RNA, code for protein

-rRNA = ribosomal RNA, form basic structure of ribosome and catalyze protein synthesis

-tRNA = tranfer RNA, central to protein synthesis as adaptors between mRNA and amino acids

-snRNA = small nuclear RNA, function an variety of nuclear process

-snoRNA = small nucleolar RNA, used to process and chemically modify rRNA

-scaRNA = small cajal RNA, used to modify snoRNA and snRNA

-miRNA = microRNA, regulate gene expression typically by blocking translation of selective mRNA

-siRNA = small interfering RNA, turn off gene expression by directing degradation of selective mRNA and the establishment of compact chromatin structure

mRNA

References:

-Albert et al., 2008. Molecular biology of the cell. 5th ed.

-Albert et al., 2004. Essential of cell biology.

-Pollard and Earnshaw. 2004. Cell biology.