Download Genomics

Introduction to Bioinformatics II
Lecture 5
By Ms. Shumaila Azam
Exons And Introns
Genes comprise only about 2% of the human
genome.
• The rest consists of non-coding regions
– chromosomal structural integrity,
– cell division (e.g. centromere)
– regulatory regions: regulating when, where,
and in what quantity proteins are made .
• The terms exon and intron refer to coding
(translated into a protein) and non-coding DNA,
respectively.
Exons
• exons are the parts of the gene that will
represent the codons for creating the protein
• Exons are parts of DNA that are converted into
mature messenger RNA (mRNA)
Introns
• Introns lie between exons,and act as wasteful DNA, as they
are cut out before the gene is translated (turned into a
protein)
• Introns are parts of genes that do not directly code for
proteins.
• Introns are commonly found in multicellular eukaryotes,
such as humans. They are less common in unicellular
eukaryotes, such as yeast, and even rarer in bacteria.
• It has been suggested that the number of introns an
organism’s genes contains is positively related to its
complexity. That is the more introns an organism contains,
the more complex the organism is.
How introns are removed?
• Introns are present in the initial RNA transcript,
known as pre-mRNA. They need to be removed in
order for the mRNA to be able to direct the
production of proteins. Pre-mRNA, therefore,
undergoes a process, known as splicing, to create
mature mRNA.
• It is vital for the introns to be removed precisely,
as any left-over intron nucleotides, or deletion of
exon nucleotides, may result in a faulty protein
being produced.
How introns are removed?
• This is because the amino acids that make up
proteins are joined together based on codons,
which consist of three nucleotides.
• An imprecise intron removal thus may result
in a framshift, which means that the genetic
code would be read incorrectly. E.g
BOB THE BIG TAN CAT wrong intron removal
can cause OBT HEB IGT ANC AT…
RNA Splicing
• RNA splicing, also known as RNA processing,
occurs at special splice sites.
• These tend to begin with the dinucleotide GU at
the 5’ end and AG at the 3’ end.
• The process is carried out by small nuclear
ribonucleo proteins (snRNPs), which are
commonly known as snurps.
• They bind to both the 5’ and 3’ ends of the intron
and cause the intron to form a loop. The intron is
then removed from the sequence and the two
remaining exons are linked together.
RNA Splicing
Altrnative Splicing
• Alternative splicing refers to the way that
different combinations of exons can be joined
together.
• This idea was first put forward by Walter Gilbert.
• He proposed that the different permutations of
exons could produce different protein isoforms.
• These in turn would have different chemical and
biological activities.
Alternative Splicing
• There are more than 1,000,000 different human
antibodies.
• Alternative splicing refers to the different ways of
combining a gene’s exons. This can produce
different forms of a protein for the same gene.
• Alternative pre-mRNA splicing is an important
mechanism for regulating gene expression in
higher eukaryotes.
• E.g. It is now thought that between 30 and 60%
of human genes undergo alternative splicing.
Altrnative Splicing
• Moreover, it is said that many human diseases
may be connected to problems with splicing.
• Example:
– One example of a human gene that undergoes
alternative splicing is fibronectin. Over 20
different isoforms of fibronectin have been
discovered. These have all been produced from
different combinations of fibronectin gene exons.
Alternative Splicing
Immunoglobulin
• B cells produce antibody molecules called
immunoglobulin (Ig) which fall in five broad
classes.
• Diversity of Ig molecules
–DNA sequence: recombination, mutation.
–mRNA sequence: alternative splicing.
–Protein structure: post-translational
proteolysis, glycosylation.
• http://www.dnalc.org/view/16939-RNASplicing.html
Translation
• Ribosome:
– cellular factory responsible for protein
synthesis;
– a large subunit and a small subunit;
– structural RNA and about 80 different
proteins.
Translation
•transfer RNA (tRNA):
– adaptor molecule, between mRNA and
protein;
– specific anti-codon and acceptor site;
– specific charger protein, can only bind to
that particular tRNA and attach the
correct amino acid to the acceptor site.
Translation
• Initiation
– Start codon AUG, which codes for methionine,
Met.
– Not every protein necessarily starts with
methionine. Often this first amino acid will be
removed in post-translational processing of the
protein.
•Termination:
– stop codon (UAA, UAG, UGA),
– ribosome breaks into its large and small subunits,
releasing the new protein and the mRNA.
Translation
Translation
• http://www.dnalc.org/resources/3d/15translation-basic.html
Post-translational processing
•Folding.
•Cleavage by a proteolytic (protein-cutting)
enzyme.
•Alteration of amino acid residues
–phosphorylation, e.g. of a tyrosine residue.
–glycosylation, carbohydrates covalently attached to
asparagine residue.
–methylation, e.g. of arginine.
•Lipid conjugation.
Control of Gene Expression
• there is strong evidence that the DNA content
of most cells in a multi-cell organism is
identical
• different cell types synthesize different sets of
proteins at different times
Control of Gene Expression
• there are at least six ways to control protein
expression
1. control when and how often a gene is
transcribed
2. control how the transcript is spliced
3. select which mRNA's are exported from
the nucleus
4. control translation
Controlling Expression
5. selectively destabilize mRNAs in the
cytoplasm
6. control protein activity (degradation,
inactivate, isolate), post-translational
modifications
• for most genes transcriptional control is the most
important
• for many diseases specific patterns of gene
expression (mRNA expression) have been
associated with the different phenotypes