gene expression and its ragulation, genomic organization,

1. •The hereditary material i.e. DNA(deoxyribonuclic acid) of
an organism is composed of an array of arrangementof
four nucleotides in a specific pattern.
•These nucleotides present an inherent information as a
function of their order.
•The genome of all organisms (except some viruses and
prions) is composed of one to multiple number of these
DNA molecule

2.  Organisms have a vast array of ways in which their
respective genomes are organized.
 A comparison of the genomic organization of six major
model organisms shows size expansion with the
increase of complexity of the organism.
 There is a more than 300-fold difference between the
genome sizes of yeast and mammals, but only a
modest 4- to 5-fold increase in overall gene number .
 However, the ratio of coding to non-coding and
repetitive sequences is indicative of the complexity of
the genome: The largely "open" genomes
of unicellular fungi have relatively little non-
coding DNA compared with the
highly heterochromatic genomes
of multicellular organisms.

4.  It is the process by which information from a gene is
used in the synthesis of a functional gene product.
 These products are often proteins, but in non-protein
coding genes such as transfer RNA (tRNA) or small
nuclear RNA (snRNA) genes, the product is a
functional RNA.
 The process of gene expression is used by all known
lifes—eukaryotes(including multicellular
organisms), prokaryotes (bacteria and archaea), and
utilized by viruses—to generate
the macromolecular machinery for life.

5. 1) TRANSCRIPTION
2) NON-CODING RNA MATURATION
3) RNA EXPORT
4) TRANSLATION
5) FOLDING
6) TRANSLOCATION
7) PROTEIN TRANSPORT

6. 1) TRANSCRIPTION
 Gene is a stretch of DNA
that encodes information. Genomic DNA
consists of two antiparallel and reverse
complementary strands.
 Each having 5' and 3‘ ends. With respect to a
gene, the two strands may be labeled the
"template strand," which serves as a blueprint
for the production of an RNA transcript, and
the "coding strand," which includes the DNA
version of the transcript sequence.

7. 2)Non-coding RNA maturation
 In most organisms non-coding genes (ncRNA) are
as precursors that undergo further processing. In
the case of ribosomal RNAs (rRNA), they are often
transcribed as a pre-rRNA that contains one or
more rRNAs. The pre-rRNA is cleaved and
modified (2′-O-methylation
and pseudouridine formation) at specific sites by
approximately 150 different small nucleolus-
restricted RNA species, called snoRNAs. SnoRNAs
associate with proteins, forming snoRNPs. While
snoRNA part basepair with the target RNA and
thus position the modification at a precise site, the
protein part performs the catalytical reaction.

8. 3)RNA export
 In eukaryotes most mature RNA must be
exported to the cytoplasm from the nucleus.
While some RNAs function in the nucleus,
many RNAs are transported through
the nuclear pores and into the cytosol.
 Notably this includes all RNA types involved
in protein synthesis. In some cases RNAs are
additionally transported to a specific part of
the cytoplasm, such as a synapse they are
then towed by motor proteins that bind
through linker proteins to specific sequences
(called "zipcodes") on the RNA.

9. 4) TRANSLATION
 For some RNA (non-coding RNA) the mature
RNA is the final gene product. In the case of
messenger RNA (mRNA) the RNA is an
information carrier coding for the synthesis of
one or more proteins.
 mRNA carrying a single protein sequence
(common in eukaryotes)
is monocistronic whilst mRNA carrying
multiple protein sequences (common in
prokaryotes) is known as polycistronic.

10. 5)FOLDING
 polypeptide folds into its characteristic and
functional three-dimensional structure from
a random coil.
 Each protein exists as an unfolded polypeptide or
random coil when translated from a sequence
of mRNA into a linear chain of amino acids. This
polypeptide lacks any developed three-
dimensional structure .
 Amino acids interact with each other to produce a
well-defined three-dimensional structure, the
folded protein known as the native state. The
resulting three-dimensional structure is
determined by the amino acid sequence .

11. 6)Translocation
 Secretory proteins of eukaryotes or prokaryotes
must be translocated to enter the secretory
pathway. Newly synthesized proteins are
directed to the eukaryotic Sec61 or prokaryotic
SecYEG translocation channel by signal
peptides. The efficiency of protein secretion in
eukaryotes is very dependent on the signal
peptide which has been used.

12. 7)Protein transport
 Many proteins are destined for other parts of the cell
than the cytosol and a wide range of signalling
sequences or (signal peptides) are used to direct
proteins to where they are supposed to be. In
prokaryotes this is normally a simple process due to
limited compartmentalisation of the cell. However, in
eukaryotes there is a great variety of different targeting
processes to ensure the protein arrives at the correct
organelle.
 Not all proteins remain within the cell and many are
exported, for example, digestive
enzymes, hormones and extracellular matrix proteins.
In eukaryotes the export pathway is well developed
and the main mechanism for the export of these
proteins is translocation to the endoplasmic reticulum,
followed by transport via the Golgi apparatus.

13.  Regulation of gene expression refers to the control
of the amount and timing of appearance of the
functional product of a gene.
 Control of expression is vital to allow a cell to
produce the gene products it needs when it needs
them; in turn, this gives cells the flexibility to
adapt to a variable environment, external signals,
damage to the cell, and other stimuli.
 More generally, gene regulation gives the cell
control over all structure and function, and is the
basis for cellular
differentiation, morphogenesis and the versatility
and adaptability of any organism.

14.  Numerous terms are used to describe types of genes
depending on how they are regulated; these include:
 A constitutive gene is a gene that is transcribed continually
as opposed to a facultative gene, which is only transcribed
when needed.
 A housekeeping gene is a gene that is required to maintain
basic cellular function and so is typically expressed in all cell
types of an organism. Examples include actin and ubiquitin.
 Some housekeeping genes are transcribed at a relatively
constant rate and these genes can be used as a reference
point in experiments to measure the expression rates of
other genes.
 A facultative gene is a gene only transcribed when needed
as opposed to a constitutive gene.
 An inducible gene is a gene whose expression is either
responsive to environmental change or dependent on the
position in the cell cycle.

15.  Regulation of transcription can be broken down into three main
routes of influence; genetic (direct interaction of a control factor
with the gene), modulation interaction of a control factor with the
transcription machinery and epigenetic (non-sequence changes in
DNA structure that influence transcription).
 The lambda repressor transcription factor (green) binds as a dimer
to major groove of DNA target (red and blue) and disables
initiation of transcription.
 Direct interaction with DNA is the simplest and the most direct
method by which a protein changes transcription levels. Genes
often have several protein binding sites around the coding region
with the specific function of regulating transcription. There are
many classes of regulatory DNA binding sites known
as enhancers, insulators and silencers. The mechanisms for
regulating transcription are very varied, from blocking key
binding sites on the DNA for RNA polymerase to acting as
an activator and promoting transcription by assisting RNA
polymerase binding.

16.  Direct regulation of translation is less prevalent than control of
transcription or mRNA stability but is occasionally used.
Inhibition of protein translation is a major target
for toxins and antibiotics, so they can kill a cell by overriding
its normal gene expression control. Protein synthesis
inhibitors include the antibiotic neomycin and the toxin ricin .
Protein degradation
 Once protein synthesis is complete, the level of expression of
that protein can be reduced by protein degradation. There are
major protein degradation pathways in all prokaryotes and
eukaryotes, of which the proteasome is a common component.
An unneeded or damaged protein is often labeled for
degradation by addition of ubiquitin.

17.  Measuring gene expression is an important part of
many life sciences, as the ability to quantify the
level at which a particular gene is expressed within
a cell, tissue or organism can provide a lot of
valuable information. For example, measuring
gene expression can:
 Identify viral infection of a cell (viral
protein expression).
 Determine an individual's susceptibility
to cancer (oncogene expression).
 Find if a bacterium is resistant to penicillin (beta-
lactamase expression

18.  Small interfering RNA (siRNA), sometimes known
as short interfering RNA or silencing RNA, is a
class of double-stranded RNA molecules, 20-
25 base pairs in length, similar to miRNA, and
operating within the RNA interference (RNAi)
pathway .
 . It interferes with the expression of specific genes
with complementary nucleotide sequences by
degrading mRNA after
transcription preventing translation.

19. 1) Long dsRNA (which can come from hairpin,
complementary RNAs, and RNA-dependent RNA
polymerases) is cleaved by an endo-ribonuclease
called Dicer. Dicer cuts the long dsRNA to form short
interfering RNA or siRNA; this is what enables the
molecules to form the RNA-Induced Silencing
Complex (RISC).
2) Once siRNA enters the cell it gets incorporated into
other proteins to form the RISC.
3) Once the siRNA is part of the RISC complex, the siRNA
is unwound to form single stranded siRNA.
4) The strand that is thermodynamically less stable due to
its base pairing at the 5´end is chosen to remain part of
the RISC-complex

20.  One of the biggest challenges to siRNA and RNAi
based therapeutics is intracellular delivery.
 Delivery of siRNA via nanoparticles has shown
promise.siRNA oligos in vivo are vulnerable to
degradation by plasma and tissue nucleases and have
shown only mild effectiveness in localized delivery
sites, such as the human eye.Delivering pure DNA to
target organisms is challenging because its large size
and structure prevents it from diffusing readily
across membranes . siRNA oligos circumvent this
problem due to their small size of 21-23 oligos.This
allows delivery via nano-scale delivery vehicles called
nanovectors.

21.  A microRNA ( miRNA) is a small non-coding
RNA molecule (containing about 22 nucleotides) found
in plants, animals and some viruses, that functions
in RNA silencing and post-transcriptional regulation of
gene expression.
 Encoded by nuclear DNA in plants and animals and
by viral DNA in certain viruses whose genome is based
on DNA, miRNAs function via base-pairing with
complementary sequences within mRNA molecules.
 As a result, these mRNA molecules are silenced, by one
or more of the following processes:
(1) Cleavage of the mRNA strand into two pieces,
(2) Destabilization of the mRNA through shortening
of its poly(A) tail,
(3) Less efficient translation of the mRNA into
proteins by ribosomes

22.  It is useful in
A. Biogenesis and molecular mechanisms
B. Cancer and inflammation
C. Cardiovascular development and
D. Pathogenesis of endocrine treatment

23.  Gene mapping describes the methods used to
identify the locus of a gene and the distances
between genes.
 The essence of all genome mapping is to place a
collection of molecular markers onto their
respective positions on the genome.
 Molecular markers come in all forms. Genes can
be viewed as one special type of genetic markers
in the construction of genome maps, and mapped
the same way as any other markers.
 There are two distinctive types of "Maps" used :
1) Genetic maps
2) Physical maps.

24.  While both maps are a collection of genetic
markers and gene loci, genetic maps' distances are
based on the genetic linkage information.
 while physical maps use actual physical distances
usually measured in number of base pairs.
 While the physical map could be a more "accurate"
representation of the genome, genetic maps often offer
insights into the nature of different regions of the
chromosome,
 e.g. the genetic distance to physical distance ratio
varies greatly at different genomic regions which
reflects different recombination rates, and such rate is
often indicative of euchromatic (usually gene-rich) vs
heterochromatic (usually gene poor) regions of the
genome.

25.  Gene sequencing is sometimes mistakenly referred to
as "genome mapping" by non-biologists.
 The process of "shotgun sequencing" resembles the
process of physical mapping: it shatters the genome
into small fragments, characterizes each fragment, then
puts them back together (more recent sequencing
technologies are drastically different). While the scope,
purpose and process are totally different, a genome
assembly can be viewed as the "ultimate" form of
physical map, in that it provides in a much better way
all the information that a traditional physical map can
offer.

26.  Use
 Identification of genes is usually the first step in
understanding a genome of a species; mapping of
the gene is usually the first step of identification of
the gene. Gene mapping is usually the starting
point of many important downstream studies.
 Disease association[
 The process to identify a genetic element that is
responsible for a disease is also referred to as
"mapping".
 If the locus in which the search is performed is
already considerably constrained, the search is
called the fine mapping of a gene. This information
is derived from the investigation of disease
manifestations in large families (genetic linkage) or
from populations-based genetic association studies.