First stage
Biology
Lec-1
2/12/2015
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Molecular Biology
Molecular biology concerns the molecular basis of biological activity between the
various systems of a cell, including the interactions between the different types of
DNA, RNA and proteins and their biosynthesis, and studies how these interactions are
regulated.
Definitions:
Genetics: Study of inherited variations.
Gene: A sequence of DNA that instructs a cell to produce a particular protein.
Allele: Alternate forms of a gene that occur at a given locus in chromosome.
Homozygous: having two identical alleles of a gene (TT or tt).
Heterozygous: having two different alleles of a gene (Tt).
Phenotype: The expression of a gene in traits or symptoms.
Genotype: The alleles combinations in an individual that cause particular traits or
disorders.
The structure of DNA and RNA
In most organisms, the primary genetic material is double-stranded DNA.
Nucleic acids are heteropolymers composed of monomers known as nucleotides; a
nucleic acid chain is therefore often called a polynucleotide. The monomers are
themselves made up of three components: a sugar, a phosphate group, and a
nitrogenous base. The two nucleic acids are polymers composed of nucleotides; DNA
is deoxyribonucleic acid, RNA is ribonucleic acid. Types of nucleic acid (DNA and
RNA) are named according to the sugar component of the nucleotide, with DNA
having 2-deoxyribose as the sugar (hence DeoxyriboNucleicAcid) and RNA having
ribose (hence RiboNucleicAcid). The sugar/phosphate components of a nucleotide are
important in determining the structural characteristics of polynucleotides, and the
nitrogenous bases determine their information storage and transmission
characteristics. The nitrogenous bases are the important components of nucleic acids
in terms of their coding function. In DNA the bases are as listed in Section 2.4,
namely adenine (A), guanine (G), cytosine (C), and thymine (T).
In RNA the base thymine is replaced by uracil (U), which is functionally
equivalent. Chemically adenine and guanine are purines, which have a double-ring
structure, whereas cytosine and thymine (and uracil) are pyrimidines, which have a
single-ring structure. The bases are held together by hydrogen bonds, two in the case
of an A = T base pair and three in the case of a G ≡ C base pair. The structure and
base-pairing arrangement of the four DNA bases.
RNA is also most commonly single stranded, although short stretches of
double-stranded RNA may be found in self-complementary regions. There are four
main types of RNA molecule found in cells: messenger RNA (mRNA), ribosomal
RNA (rRNA), smallnuclear RNA (snRNA) and transfer RNA (tRNA). Ribosomal
RNA is the most abundant class of RNA molecule, making up some 85% of total
cellular RNA. It is associated with ribosomes, which are an essential part of the
translational machinery. Transfer RNAs make up about 10% of total RNA and
provide the essential specificity that enables the insertion of the correct amino acid
into the protein that is being synthesized. Messenger RNA, as the name suggests, acts
as the carrier of genetic information from the DNA to the translational machinery and
usually makes up less than 5% of total cellular RNA.
The anatomy of gene
Although there is no such thing as a ‘typical’ gene, there are certain basic
requirements for any gene to function. The most obvious is that the gene has to
encode the information for the particular protein (or RNA molecule). The double-
stranded DNA molecule has the potential to store genetic information in either strand,
although in most organisms only one strand is used to encode any particular gene.
There is the potential for confusion with the nomenclature of the two DNA strands,
which may be called coding/non-coding, sense/antisense, plus/minus, transcribed/non-
transcribed, or template/non-template. A site for starting transcription is required, and
this encompasses a region that binds RNA polymerase known as the promoter (P),
and a specific start point for transcription (TC). A stop site for transcription (tC) is
also required. From TC start to tC stop is sometimes called the transcriptional unit,
that is, the DNA region that is copied into RNA. Within this transcriptional unit there
may be regulatory sites for translation, namely a start site (TL) and a stop signal (tL).
Other sequences involved in the control of gene expression may be present either
upstream or downstream from the gene itself.
Gene structure in prokaryotes
In prokaryotic cells such as bacteria, genes are usually found grouped together
in operons. The operon is a cluster of genes that are (often coding for enzymes in a
metabolic pathway) and that are under the control of a single promoter/regulatory
region. Perhaps the best known example of this arrangement is the lac operon (Fig.
2.7), which encodes for the enzymes responsible for lactose catabolism. The fact that
structural genes in prokaryotes are often grouped together means that the transcribed
mRNA may contain information for more than one protein. Such a molecule is known
as a polycistronic mRNA, with the term cistron equating to the ‘gene’ as we have
defined it (i.e. encoding one protein). Thus, much of the genetic information in
bacteria is expressed via polycistronic mRNAs whose synthesis is regulated in
accordance with the needs of the cell at any given time. This system is flexible and
efficient, and it enables the cell to adapt quickly to changing environmental
conditions.
Gene structure in eukaryotes
A major defining feature of eukaryotic cells is the presence of a membrane-
bound nucleus, within which the DNA is stored in the form of chromosomes.
Transcription therefore occurs within the nucleus and is separated from the site of
translation, which is in the cytoplasm. Gene structure and function in eukaryotes are
more complex than in prokaryotes. Eukaryotic genes contained ‘extra’ pieces of DNA
that did not appear in the mRNA that the gene encoded. These sequences are known
as intervening sequences or introns, with the sequences that will make up the mRNA
being called exons.
DNA Replication :
• Replication of DNA is semiconservative .
• During replication the 2 complementary strand unwind and each single strand
serve as template directing the synthesis of a new complementary strand .
• The new result of replication is thus 2 progeny DNA molecules identical to the
parental double helix . A site where DNA is locally opened called replication
fork .
Enzymes involved in DNA replication and their function :
1. Helicase : unwinds parental double helix .
2. Binding Proteins : stabilize separate strands .
3. Primase : adds short RNA Primer to template strand .
4. DNA Polymerase :
Adding bases to the new DNA chain , added Bases in (5'→3') direction only
and DNA is antiparallel, the new strand is synthesized continuously in (5'→3')
direction called Leading strand, while the other daughter strand is synthesized
discontinuously by short segments of DNA called Okazaki Fragments (5'→3')
that are joined together by ligase and called Lagging strand .
Proofreading activity checks and replaces incorrect bases .
Removing RNA primer .
5. Ligase: joins okazaki fragments and seals other nicks in sugar phosphate
backbone .
Electron micrograph of a eukaryote replicating fork demonstrating the presence of
histone- protein containing nucleosomes on both branches.
Genome:
A genome is an organism's complete set of deoxyribonucleic acid (DNA), a
chemical compound that contains the genetic instructions needed to develop and
direct the activities of every organism. The human genome contains approximately
3.2 billion of base pairs, which reside in the 23 pairs of chromosomes (22 autosome
pairs + 2 sex chromosomes) in the haploid genome. Human genome comprise of
around 30,000 - 40,000 genes. Only about 3% of human genome codes for proteins
while 40-50% is repetitive DNA and others is unknown function.