Genetics Notes - 30600 PDF

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ANKUSH SHARMA BIO 20300 NOTES

Lecture 9 Chapter 4 Loss of function and gain of function.

Mutations ultimately provide a phenotype, a mutant phenotype that is a disruption of the process that can lead to an outcome that’s visible and that can be analyzed. Wild type situation (diploid organisms like mammalian cells here). There are two alleles because there are two homologous chromosomes. Two copies of each gene-one maternal and one paternal (or rRNA or tRNA as well instead of protein). What happens if there is a point mutation that disrupts the function of the gene? Loss of function here. Gene of function is disrupted, and production of damaged or functionally inactive protein. In the case of homozygous, no production of functional proteins. In the case of heterozygous, one allele mutated and one allele that’s functional, if the mutation is recessive, you will not detect any mutant phenotype. Loss of function mutation or poorly functional mutation. Loss of function mutation usually predicted to be recessive, because the wildtype protein if produced can compensate. All the terms mean the same thing. Deleterious mutation that leads to the loss of function.

Special case of loss of function is complete loss of function. That’s done when you get rid of the gene activity all together. You can do that by performing a complete deletion of the gene. That can occur naturally. You completely delete the genes. It can be done artificially as well. In the homozygous case, no gene product. In heterozygous, one copy (wild copy) that is oong producing any protein at all (?). This is null or deletion. Amorphic he never heard of. This is the holy grail for genetic analysis, because you are leaving no genetic activity for a specific gene. Null is what people in genetics are trying to obtain. This is not always possible tho. Not all genes can be deleted like this. Some genes are never subjected to a homozygous null. YOu never get that, because if you delete both, the cell or the organism is dead. An essential gene is a gene that cannot be deleted without compromising the gene. You can increase the gene activity. Called gain of function. Hypermorphic. You can simply mutate the promoter, you can convert tata box into a better promoter and the locus is not affected but it leads to a higher transcription and then you can overproduce the protein. Gain of function phenotype. You can induce it also by modifying the protein so that it attains increased activity. Excessive gene action. Predicted to be dominant, because the mutated protein will exert its function in presence of the wildtype protein.

Neomorphic mutations-seen in multicellular organisms and flies. Special kind of mutation that produces a new function. In drosophila-a leg instead of antennae. _ -THis is due to the transcription factor being active in certain tissue types when normally that transcription factor is not active. Predicted to be dominant usually.

Told us that if there is a deleterious mutation, then it’s usually recessive. But not always the case-deleterious mutations that are dominant exist-dominant negative mutations. These are gene products that work in a complex-subunit part of a protein complex that assembles after translation. Think of mutated, toxic subunits coming into the complex. When it assembles with the second gene product it interacts, it assembles and has a poisonous effect on the whole complex and the process doesn’t work or doesn't work normally. Often observed in multimeric proteins. There are some DNA binding proteins that assemble and they form together a high affinity DNA binding domain for a specific sequence. You can mutate one of the subunits, it will still assemble, but it prevents the whole thing from assembling on the DNA-this would be an example of dominant negative mutation. This type of mutation is more common than we think. Loss of function-enzyme inactive or works much slowly as compared to wild type. Related, but not always. Dominant negative is dominant even though it’s a loss of function.

Null-in the heterozygous situation, he made an assumption 50% of the gene activity is enough to provide function. In a significant number of times, 50% of gene activity is not enough to fully perform the function of the gene 30% of the times. You will see a phenotype because you don’t have enough gene activity coming from the wildtype copy of the gene. This is another exception to the loss of function is usually recessive rule.

Penetrance-mutation has a great effect vs as large an effect. Highly penetrant or weakly penetrant. Not going to be asked about codominance-not going to be quizzed. If you have a mutation over wildtype and you see a phenotype, that’s called a dominant mutation.

If you have one locus, you don’t necessarily have one functional allele for that locus-there may be several that provide different phenotypes. And they are considered wild type because there are part of overall population at a frequency that’s usually over 1% of total number of alleles. Mutation is a lot less common than that. It’s not considered part of the alleles. There are some loci that have different number of alleles that lead to different phenotypes. You can have IA, IB, and II in blood group locus that codes for H antigen.

Which one is the wild type?

All wildtypes.

C locus in rabbits. Some mutations might have arose and became fixed allele. Himalayan allele-pigment produced only in the colder temperature region. Albino-all white. Dominant recessive relationship exists.

For certain loci, there are a number of different alleles in a population, which are called allelic series.

Another type of mutation here called recessive lethal. These type of mutations is a mutation that is lethal at homozygosity. Homozygous mutant dead. Agouti wildtype, yellow mutant. Yellow due to excessive production of yellow pigment.

Explanation at the molecular level. Large gene deletion leads to AY allele. Agouti gene under control of the Raly promoter. Since it is a stronger promoter, it leads to the hyperproduction of the yellow pigment. At the same time, it takes out the Raly gene, which is required for viability. Homozygous Ay thus dies. Notion of essential gene.

Mutations are important for genetic analysis, and when you work on the model system in the lab, the genetic approach is to obtain mutation with an interesting phenotype such that the mutation can tell you about what the gene does. They are tool in research.

Using fungus. Beadle and Tatum did it to understand pathways. It is haploid, so you don’t worry about homozygosity or anything. Just single copy. You mutagenize the fungus with X rays, and randomly pick spores and let them grow in complete medium and minimal medium-does not contain any amino acids, vitamin, etc. You are looking for mutants that can grow in complete but cannot grow in minimal. You take that mutant from the complete and passage it in many different test media. When you add in amino acids, it grows, so it was missing the ability to synthesize amino acids. You test all twenty amino acids. Then you realize addition of methionine makes it grow. So it lacked the ability to synthesize methionine.

Inability to grow methionine because it’s missing an enzyme in some part of the pathway. Which intermediate was accumulating? Met 1 accumulates homocysteine. So the step not functioning for Met is the conversion from homocysteine to methionine. If that’s true, then the mutant in question would be rescued by addition of the metabolite that comes after the block. If you add methionine, there is growth, but if you add anything else, there is no growth. For met3, if you add cystathionine or anything else downstream of that, there is growth.

Dihybrid crosses. 9 different genotypes, phenotypic ratio-9331. It occurs only when the two phenotypes are completely independent of one another. For ex, shape and color two completely independent processes, which is why you have 9331. If there are interactions, epistasis. Genotypes all the same, but epistasis (interaction in terms of contribution to the phenotype) can lead to different phenotypic ratio.

Color of the flower. Turns out that the purple color is produced by a pathway with number of different enzymes that lead to anthocyanin. If it is not produced, you get white flower. Two genes essential for producing anthocyanin. One C acting between steps 1 and 2, and P between precursor II and anthocyanin. You can have either mutant in C or P. Homozygous mutant in either C or P lead to white. Complementary gene interaction-linear sequence of enzymes that produce the pigment in this case.

Duplicate gene action. Case of redundancy. Enzymes do the same thing. P and R both lead to anthocyanin. Either P or R lead to anthocyanin. Only in homozygous P and R double mutant, you produce white.

Dominant gene interactions.Two parallel pathways. If you have either gene action, you get sphere, and you need both genes to act to get disk. Double mutant is long. 9:6:1

The genes do different things. E important for deposition of the pigment, and B produces the pigment.

Not asked

Not asked

Cross two homozygous mutant flies that carry m1 and m2. No complementation-you will recover the mutant phenotype. Indicative that two alleles you are testing are affecting the same locus. If they happen to affect different loci, then in the F1, heterozygous for both genes. You will recover the wild type phenotype.

You have mutant called apricot and homozygous crosses with homozygous brown, buff, etc, or independent mutations that affect the color of the eyes, and for example, there is no complementation between apricot and cherry, which means that apricot and cherry are on the same gene. Mutations apricot, cherry, and white are three allele of the gene white. Brown in a locus by itself. All the ones in white complementation group are mutations that are independently obtained that are all alleles of white. 5 different loci or complementation group.

Lecture 10

Linkage is the association of two genes on the same chromosome arm that segregates together in meiosis. They don’t randomly assort in gametes. Unlinked genes are on different chromosomes and independently assort. Genes that are located on the same chromosome are called syntenic genes. When two syntenic genes are so close to one another that their alleles are unable to assort independently, the genes display genetic linkage Homologous recombination is the process that occurs as a result of crossing over in prophase I of meiosis in eukaryotic cells. It takes place through the equal exchange of genetic material contained in homologous chromosomes At the end of meiosis the outcome is the generation of recombinant chromosomes or nonparental chromosomes that come about by the reshuffling of alleles residing on recombining chromosome. Syntenic genes located very near each other on a chromosome tend to recombine less often during crossing over than do genes located farther apart on the chromosome.

Unlinked genes associated independently. But if you have linkage (genes associated on the chromosomes) in the same chromosome they are linked. This is detected because gametes contain this association unless they are separated in meiosis 1. Linked genes can segregate together in meiosis. Linked are also found close together on the same chromosome arm. Separation by recombination will be seen in a small proportion of the progeny. Linked genes are always syntenic, and they are always located near one another on a chromosome. Syntenic genes are so far apart on the chromosome that crossing over between them generates an independent assortment of the alleles, the genes are not linked. Genetic linkage leads to the production of a significantly greater number of gametes containing chromosomes with parental combinations of alleles than would be expected under assumptions of independent assortment, and to a significantly smaller number of gametes containing chromosomes with alleles that are different from the parental combinations. Crossing over is less likely to occur between linked genes that are close to one another than between genes that are farther apart on a chromosome.

Lecture 11

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Lecture 14

Lecture 15

Lecture 16

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