Molecular Biology I

DNA structure

Genome
The total number of genes in one cell constitutes the genome of the cell. There are about 3 X 109 base pairs (bp) in each human haploid genome. They are distributed in 23 chromosomes. Only 10% of the total human genes are functioning genes.

Gene: It is a deoxyribonucleic acid (DNA) segment, or in some viruses a ribonucleic acid (RNA) segment that contains a well defined genetic information. The genes are carried on chromosomes. Because chromosomes are paired, everybody carries two copies of each gene.

Gene Expression

DNA

Transcription

mRNA

Translation

protein

Replication

DNA Replication
Definition: It is the process of DNA synthesis using parent DNA strands as template. It aims at formation of a copy of the parent DNA molecule for the daughter cell

Stages of DNA replication in eukaryotes

I- Initiation II- Elongation III- Termination

Initiation of DNA replication

1- Identification of the origins of replication 2- Unwinding of double stranded DNA 3- Formation of replication forks 4- RNA primer synthesis

Identification of the origin of replication

Formation of replication fork

Formation of Replication fork

Unwinding of double stranded DNA

Elongation of DNA replication

1- Leading strand synthesis 2- Lagging strand synthesis

Termination of DNA replication

Rules of DNA replication in eukaryotes

1- DNA replication is semiconservative 2- Replication begins at multiple origins and usually bidirectionally 3- Replication exhibits polarity 4- Replication is very accurate 5- DNA replication occurs in the nucleus during the synthetic phase of eukaryotic cell cycle

Basic requirements for DNA replication

1- Substrates: The four deoxynucleotide triphosphates 2- Template 3- Primer: DNA polymerases are unable to start DNA synthesis except in the presence of pre-existing primer 4- Enzymes: helicase, topoisomerases, DNA polymerases and ligases

DNA Repair
It is a mechanism to repair damaged DNA DNA is subject to damage by a wide variety of agents. Therefore, the presence of a mechanism of DNA repair to maintain the genetic information is very important. If the damage is not repaired, a permanent mutation may be introduced that can result in serious effects.

Causes of DNA damage

1- Spontaneous changes:- e.g. *Deamination of cytosine to uracil. * Depurination. 2- DNA polymerase errors:- e.g. 2-amino purine incorporated instead of adenine into a newly synthesized DNA strand. 3- radiation damage: * U.V. * Ionizing radiation (X-ray, -rays).

4- Chemicals: * Nitrous acid ( HNO2). * Alkylating agents such as dimethyl sulfate 5- Oxidative damage by: * H2O2. * Hydroxyl radicals. 6- Carcinogenic compounds in food, water or air e.g. * Aflatoxin * Chemical (in cigarette smoke).

Types of DNA Repair

1- Mismatch repair. 2- Base excision repair. 3- Nucleotide excision repair. 4- Double strand break repair

Defects in DNA Repair Cause Human Diseases

Xeroderma Pigmentosa: It is an autosomal recessive disease. The most common deficiency occurs in the excision endonuclease enzyme. It is characterised by extreme sensitivity to sunlight, ulceration and skin cancer

Transcription
It is the process of synthesis of RNA from a DNA template by RNA polymerase enzymes and a number of associated proteins

Basic features of RNA synthesis

1- The precursors of RNA synthesis are the four ribonucleotide 5`- triphosphates. 2- The RNA chain grows in the 5` 3` direction which is the same as the direction of chain growth in DNA synthesis

3- RNA polymerases, in contrast with DNA polymerases, can initiate RNA synthesis , no primer is needed 4- Contrary to DNA replication, only one strand is transcribed, unwinding is limited to the transcribed gene segment

Steps of RNA synthesis

1- Initiation 2- Elongation 3- Termination

son of DNA synthesis (replication) and RNA synthesis (transcrip

Replication
* Definition * Character DNA synthesis from DNA template.

Transcription
RNA synthesis from DNA template.

Complete Selective (The entire chromosome is normally (Only particular genes are copied). transcribed at any one time, and some portions of the DNA genome are never transcribed). The two DNA strands serve as template. DNA polymerase enzyme (DNA polymerase cannot initiate strand synthesis). Required d ATP, d GTP, d CTP and d TTP Only one of the two strands serves as template. RNA polymerase. (RNA polymerase can). Not required ATP, GTP, CTP, UTP

* Template * Polymerization

- RNA primer - Required substrates

- Direction of synthesis

5`

3`

5`

3`

- proofreading Present activity (3` 5` (high fidelity DNA synthesis). exonuclease).

Absent (low- fidelity RNA synthesis).

Post- transcriptional modification of RNA

Processing of eukaryotic mRNA precursor: 1- Capping 2- Polyadenylation 3- Splicing

(1) Capping:The cap (7-methyl guanosine) is added to the 5` end while the RNA molecule is still being synthesized. 7- methyl guanosine is joined to the 5` end of mRNA in an unusual 5`, 5` - triphosphate linkage. Significance of the cap structure:Serves as a ribosome binding site (for translation initiation). Protects the 5` end of mRNA from attack by 5` 3` exonuclease (for mRNA stability).

(2) Polyadenylation:Poly (A) polymerase enzyme adds poly (A) tail to the 3`end of mRNA (which is short at first about 20A residues , then subsequently extended to as much as 200 A residues). Significance of the poly (A) tail:Protects the 3` end of mRNA from 3` 5` exonuclease attack (for mRNA stability). Aids in its transport from nucleus to cytoplasm.

(3) Splicing:Splicing means removal of introns from the primary transcript in the nucleus and then ligation of exons to form mature functional m RNA. The mature mRNA is then transported to the cytoplasm where it is translated into protein

II Processing of eukaryotic ribosomal RNA precursor (pre- r RNA):Eukaryotic rRNA is transcribed in the nucleolus by RNA polymerase I as a single piece of 45 S RNA precursor (pre- rRNA) Then it is subsequently cleaved to yield 28 S rRNA, 18 S rRNA, and 5.8 S rRNA. RNA polymerase III transcribes the 5S rRNA unit from a separate gene.

III Processing of eukaryotic transfer RNA precursor (pre- tRNA):Eukaryotic tRNA genes are all transcribed by RNA polymerase III. The primary transcript (pre- tRNA) requires posttranscriptional processing to be mature functional tRNA such as:- Folding and base pairing to generate its characteristic shape. - Removal of excess nucleotides from the 5` and 3` ends (cleavage).

- Removal of introns (splicing). - Addition of the CCA sequence at 3` end. - Modification of some bases by methylation, deamination or reduction.