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STRUCTURE OF GENEGene – “a segment of DNA that is expressed to yield a functional protein.”
“Gene” term coined by Johanson ( 1909).
Eukaryotic genes are split genes.
INTRONSAn intron is a DNA region within a gene that
is not translated into protein. Discovered by Richard Roberts and Phillip
Sharp (1977) during the studies of adenoviral replication in cultured humans cells.
Have no cellular functionsHave helped accelerate evolution by
facilitating recombination between exons of different genes- “EXON SHUFFLING”.
Introns early viewIntrons late view
Eukaryotic Promoters - in Contrast A promoter is a
regulatory region of DNA located upstream (towards the 5' region) of of a gene, providing a control point for regulated gene transcription.
The promoter contains specific DNA sequences that are recognized by proteins known as transcription factors.
PROMOTER ELEMENTS Core promoter - the minimal portion of the promoter required to
properly initiate transcription
Transcription Start Site (TSS) Approximately -34 A binding site for RNA polymerase General transcription factor binding site
Proximal promoter - the proximal sequence upstream of the gene that tends to contain primary regulatory elements. Approximately -250 Specific transcription factor binding sites
TATA box (sequence TATAAA), which in turn binds a TATA binding protein which assists in the formation of the RNA polymerase transcriptional complex.
ENHANCERS discovered by Walter Schaffner (1981)
during studies of the SV40 viral promoters.Stimulate transcription when placed either
upstream / downstream of the promoter.Binding of specific transcriptional regulatory
proteins to enhancers is responsible for the control of gene expression during
development and differentiation the response of cells to hormones and growth
factors.
SILENCERS & INSULATORS Silencers are control regions of DNA that, like enhancers, may be
located thousands of base pairs away from the gene they control.
When transcription factors bind to them, expression of the gene they control is repressed.
Insulators are stretches of DNA (as few as 42 base pairs may do the trick) located between the
enhancer(s) and promoter or silencer(s) and promoter
of adjacent genes or clusters of adjacent genes.
In mammals (mice, humans, pigs), only the allele for insulin-like growth factor-2 (IGF2) inherited from one's father is active; that inherited from the mother is not — a phenomenon called imprinting.
UNTRANSLATED REGIONS(UTR’s)Either of two sections on each side of a
coding sequence on a strand of mRNA.
Two types 5’ UTR or leader sequences 3’ UTR
MUTATION- INTRODUCTIONA mutation is a sudden change in the
amount, arrangement or structure of the DNA of an organism.
This produces a change in the genotype which may be inherited by cells derived by mitosis or meiosis from the mutant cell.
A mutation can occur at DNA level (gene mutation)or at the chromosome level( chromosomal aberrations).
REPAIR MECHANISMSCells have acquired several repair mechanisms
to maintain the integrity of their genomes.DNA repair two types
Direct reversal of chemical reations Removal of damaged bases
Base excision repair nucleotide excision repair mismatch repair
• Mutation in the repair genes results in inherited diseases.
Repair defects & human diseasesDefect in nucleotide
excision repair results in xeroderma pigmentosum, cockayne’s syndrome, trichothiodystrophy.
Defect in mismatch repair results in hereditary nonpolyposis colorectal cancer.
DNA REARRANGEMENTS Transposons are
sequences of DNA that can move or transpose themselves to new positions within the genome of a single cell.
Transposition of both LINES & Alu elements – haemophilia, muscular dystrophy & colon cancer.
GENE MUTATIONone allele of a gene changes into a different allele.Because such a change takes place within a single
gene and maps to one chromosomal locus (“point”), a gene mutation is sometimes called a point mutation.
Point mutation typically refer to alterations of single base pairs of DNA or of a small number of adjacent base pairs.
At the DNA level, there are two main types of point mutational changes:
base substitutions and base additions or deletions(indels).
BASE SUBSTITUTIONMutation in which one base pair is
replaced by another.Base substitutions again can be
divided into two subtypes: transitions and transversions.
TRANSITIONS AND TRANSVERSIONS a purine base is replaced by another
purine base (A by G or G by A) or a pyrimidine by another pyrimidine (T by C or C by T) the substitution is called a transition.
If a purine base is substituted by a pyrimidine, or vice versa, the substitution is called a transversion.
Transitions are by far the most common types of mutations.
transition mutations code for chemically similar amino acids while transversions show a greater possibility of inserting amino acids with different charges.
Although transitions and transversions can cause nonsense mutations, the chances of missense mutations are greater.
SINGLE BASE SUBSTITUTIONA single nucleotide substitution within
polypeptide-encoding DNA causes defective gene expression by activating a cryptic splice site within an exon.
Single base substitution can be classified as synonymous substitution missense mutation nonsense mutation
Synonymous (silent) mutationSubstitutions results in a new codon specifying
the same aminoacid.Most frequently observed in coding DNA,
because they are almost always neutral mutations and not subject to natural pressure.
Substitution often occur at the third base position of a codon: third base wobble means that the altered codon often specifies the same aminoacid.
Base substitution at first base position can give rise to a synonymous substitution( e.g., CUA UUA, CUG UUG).
Nonsense mutationA codon specifying an
aminoacid is replaced by a stop codon (UAA, UGA, UAG).
leads to the premature termination of translation.
Stop codon mutations can occur at any positions.
E.g., DMD, β thalessemia, cystic fibrosis, hurler syndrome.
Stop codon mutationMutation that changes a stop codon into a codon
for an aminoacid.• Results in production of
too large proteins, making protein non functional and in some cases harmful proteins.
• E.g., Familial British dementia.
MISSENSE MUTATIONThe codon for one
aminoacid is replaced by another aminoacid.
2nd position- always a missense mutation
3rd position almost always a missense mutation.
Can be either conservative
substitution Non-conservative
substitution
Conservative substitutionReplacement of
aminoacid by another that is chemically similar to it.
The effect of suchsubstitutions on protein function is minimal because the side chain of the new aminoacid may be functionally similar to that of aminoacid to it replaces.
Nonconservative substitutionReplacement of one
aminoacid by another which has a dissimilar side chain, a charge difference or a polar by a non polar and vice-versa.
Often occurs in the first and second codon positions.
E.g., sickel cell anemia.
INSERTION/ DELETION MUTATIONSGain or loss of one
or more nucleotides results in frame shift mutation.
Frameshift mutation typically exhibit complete loss of normal protein structure and function.
Single & double nucleotide INDEL- all downstream aminoacid change.
Triplet INDEL- insertion / deletion of a single aminoacid produce milder consequences.
Multiple triplets produce major effect.
Multiple repeats- Trinucleotide expansion
A dynamic mutation responsible for causing any type of disorder categorized as a trinucleotide repeat disorder.
Triplet expansion is caused by slippage during DNA replication.
Due to the repetitive nature of the DNA sequence in these regions, 'loop out' structures may form during DNA replication while maintaining complementary base paring between the parent strand and daughter strand being synthesized.
Trinucleotide repeat disorders
Huntington’s diseaseThe HTT gene is located
on the short arm of chromosome 4, at 4p16.3.
HTT contains a sequence of three DNA bases—cytosine-adenine-guanine (CAG)—repeated multiple times (i.e. ... CAGCAGCAG ...), known as a trinucleotide repeat.
CHROMOSOMAL MUTATIONS Chromosomal mutations take place when
the number of chromosomes changes or when structural changes occur in the chromosomes.
occurs generally during the formation of a zygote where changes in the number of chromosomes may result in fission (two into one or one into two) or fusion (two into one).
Chromosomal anomalies
Numerical Structural
Trisomy Monosomy Triploidy Tetraploidy
Intrachromosomal Interchromosomal
Reciprocaltranslocations
Robertsonian translocations
inversions isochromosomesrings deletionsduplications
Changes in number of genes loss or deletion addition or duplication
changes in gene arrangement inversion translocation
CHANGES IN NUMBER OF GENES: Deletion mutationDeletion is a mutation
in which a part of a chromosome is missing.
Deletions can be caused by errors in chromosomal cross over during meiosis.
Deletion can be either Intercalary/ interestitial TerminalExample: cri du chat
syndrome
Deletion typesIntercalary/
interestitial - a deletion that occurs from
the interior of a chromosome.
Terminal deletion- a deletion that occurs towards the end of a chromosome.
CHANGES IN NUMBER OF GENES: DuplicationA duplication occurs
when part of a chromosome is copied (duplicated) abnormally, resulting in extra genetic material from the duplicated segment.
CHANGES IN GENE ARRANGEMENT: Inversion Inversion occurs when a
region of a chromosome breaks off and rotates through 180 degree before rejoining the chromosome.
No change in genotype occurs as a result of inversion but phenotypic changes may be seen.
Two types of inversion mutation Pericentric inversion paracentric inversion
PARACENTRIC INVERSIONS
The inversions have break points on the same side of the centromere.
Meiotic recombination in an inversion loop produces one recombined chromatid with two centromeres and another chromatid with lack of centromere.
Pericentric inversions span the centromere and crossover within the inversion loop swaps the ends of one chromatid on each chromosome, duplicating one end and deleting the other and all the chromatids have a single centromere, so they can all segregate normally at meiosis and pass into gametes
PERICENTRIC INVERSION
CHANGES IN GENE ARRANGEMENT : Translocation a rearrangement of
chromosome material involving two or more chromosomes.
Two types reciprocal (non-
robertsonian) non-reciprocal
(Robertsonian).
Reciprocal translocationsMaterial is exchanged
between two chromosomes.
translocations can occur between any of the chromosomes and involve pieces of any size.
arises when an exchange of chromosomal material takes place between two different chromosomes.
When there is no loss or gain of chromosome material, the translocation is described
as ‘balanced’.
Robertsonian translocationsInvolves exchange
between acrocentric chromosomes 13, 14, 15, 21 and 22.
The exchange involves loss of the short arms of two chromosomes and fusion of the remaining two long arms at their centromeres.
Uniparental disomy (UPD)occur when the developing embryo has
attempted to ‘correct’ a trisomy by disposing of the spare third copy of the chromosome.
This can leave the baby with two copies of the chromosome from the same parent instead of the normal balance of one copy from each parent.
Prader-Willi syndrome
When the corrected chromosome is 15 and thebaby inherits two chromosome 15s from themother, the baby will have typical features of Prader-Willi syndrome.
overweight, short stature and learning difficulties.
Angelman syndrome
When the corrected chromosome is 15 and the baby inherits two chromosome 15s from the father, the baby will have typical features of Angelman syndrome.
epilepsy, severe learning difficulties, an unsteady walk.
CHANGES IN CHROMOSOME NUMBER
Changes in chromosome number can occur by the addition of all or part of a chromosome , the loss of an entire set of chromosomes or the gain of one or more complete sets of chromosomes .
Each of these conditions is a variation on the normal diploid number of chromosomes with drastic effects on phenotypic expression.
TRISOMYA trisomy is a
genetic abnormality in which there are three copies, instead of the normal two, of a particular chromosome.
E.g., 21 trisomy, 18 trisomy.
MONOSOMYMonosomy is a
form of aneuploidy with the presence of only one chromosome(instead of the typical two in humans) from a pair.
E.g., turners syndrome.
TRIPLOIDY A baby with three copies of each chromosome in each cell rather
two, making a total of 69 chromosomes. Triploidy can result either from a single egg being fertilized by
two sperm or from an error in cell division causing either the egg or the sperm to have 46 chromosomes at the time of fertilization.
Triploidy may be the result of either digyny (the extra haploid set is from the mother) or diandry (the extra haploid set is from the father).
Diandry may be due to reduplication of the paternal haploid set from a single
sperm. dispermic (two sperm) fertilization of the egg.
Digyny is most commonly caused by either failure of one meiotic division during oogenesis leading to a
diploid oocyte or failure to extrude one polar body from the oocyte.
TETRAPLOIDY
ISOCHROMOSOMESA relatively frequent
chromosome aberration mainly in X chromosome.
The chromosomes are not divided along their length but transversely.
E.g., Pallister killan mosaic syndrome.
Pallister-Killian syndrome presence of the
anomalous extra isochromosome 12p, the short arm of the twelth chromosome.
the presence of the extra chromosome may be linked to pre meiotic mitotic errors.
As cells divide during early development, some cells lose the i12p , while others retain- mosaicism.
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