Detection of linkage



Mapping with molecular markers

Alleles used as experimental probes to keep track of an individual, a tissue, a cell, a nucleus, a chromosome, or a gene are called markers .

 In the first 70 years of building genetic maps these markers with detectible phenotype were used.

 However, even in those organisms in which the maps appeared to be “full” of loci of known phenotypic effect, measurements showed that the chromosomal intervals between genes had to contain vast amounts of DNA.

 These gaps could not be mapped by because there were no markers linkage analysis , in those regions.

 So, additional map.

genetic markers were needed, that could be used to fill in the gaps to provide a higher-resolution  Ultimately molecular markers were discovered.

 A

molecular marker

is a site of heterozygosity for some type of silent DNA variation not associated with any measurable phenotypic variation.

 Such a “DNA locus,” when heterozygous, can be used in mapping analysis.

 Because molecular markers can be easily detected and are so numerous in a genome, when they are mapped by linkage analysis, they fill the voids between genes of known phenotype.

 In this way, markers are being used just as milestones were used by travelers in previous centuries.

 Travelers were not interested in the milestones (markers) themselves, but they would have been disoriented without them.

 The two basic types of molecular markers are those based on restriction-site variation and on repetitive DNA .

Gene Mutations

Lecture 6

Dr. Attya Bhatti

Any variation in the DNA sequence is called Mutation .

• In gene mutation, an allele of a gene changes, becoming a different allele.

• As change takes place within a single gene is also called a point mutation .

• To consider change, we must have a fixed reference point, or standard.

• In genetics the wild type provides the standard.

 Any change away from the wild-type allele is called forward mutation.

 Any change back to the wild-type allele is called reverse mutation (or reversion or back mutation).

 For example,  The frequency of mutants in a population is called mutation frequency .

At DNA level mutations are of following types

Base substitutions Base additions or deletions Transitions Transversions Silent substitution Nonsense mutation Missense mutation

Gene Mutations at the Molecular Level



Synonymous substitution:

It is substitution of a chemically similar amino acid and it will have a less severe effect on the protein’s structure and function.

 Nonsynonymous substitutions: It is substitution of chemically different amino acid and is more likely to produce severe changes in protein structure and function.

 Mutations that are in or close to the mutations are called

null

active site of a protein will most likely lead to lack of function; such (nothing) mutations.  Mutations in less crucial areas of a protein will most likely have less deleterious effect, often resulting in

“leaky,”

or partly inactivated, mutants.

The effect of some common types of mutations at the RNA and protein levels

Somatic versus germinal mutation

Mutant Types:



Morphological mutations

They affect the visible properties of an organism, such as shape, color, or size.

For Example; Curly wings in Drosophila, and dwarf peas 

Lethal mutations

Lethal mutation affect the survival of the organism.

Mutant Types:



Conditional mutations:

In the class of conditional mutations, a mutant allele causes a mutant phenotype in only a certain environment, called the environment, called the restrictive condition permissive condition

.

, but causes a wild-type phenotype in some different For example, certain Drosophila mutations are known as heat-sensitive lethals . Heterozygotes (say, H condition).

dominant + /H) are wild type at 20°C (the permissive condition) but die if the temperature is raised to 30°C (the restrictive

Mutant Types:



Biochemical mutations:

They are charachterized by the loss or change of some biochemical function of the cells.

This change typically results in an inability to grow and proliferate.

For example, one class of biochemically mutant fungi will not grow unless supplied with the nitrogenous base adenine.

Mutant Types:



Loss-of-function mutations

Generally, loss-of-function (null) mutations are found to be recessive.

However, some loss-of-function mutations are dominant.

In such cases, the single wild-type allele in the heterozygote cannot provide the amount of gene product needed for the cells and the organism to be wild type.

Mutant Types:

• (a)Mutation m has completely lost its function (it is a null mutation).

• In the heterozygote, wild-type gene product is still being made, and often the amount is enough to result in a wild-type phenotype, in which case, m will act as a recessive.

• If the wild-type gene product is insufficient, the mutation will be seen as dominant.

• (b) Mutation m′ still retains some function, but in the homozygote there is not enough to produce a wild-type phenotype.

• (c) Mutation M has acquired a new cellular function represented by the gene product colored green. M will be expressed in the heterozygote and most likely will act as a dominant. The homozygous mutant may or may not be viable, depending on the role of the + allele.

Mutant Types:



Gain-of-function mutations

Mutation which will produce a new function is called gain of function mutation.

In a heterozygote, the new function will be expressed, and therefore the gain-of-function mutation most likely will act like a dominant allele and produce some kind of new phenotype.

Mutation and cancer



Cancer is a genetic disease.



Cancer has many causes, but ultimately all these causes exert their effects on a special class of genes called cancer genes or proto-oncogenes

.

Human chromosomes showing bands from Giemsa staining and the positions (shown by black dots) of known proto oncogenes; mutations in proto-oncogenes lead to cancer.

Comparison of the various outcomes of somatic mutations in proto-oncogenes and other genes.