Assignment Code: BBCCT-121/TMA/2023

Course Code: BBCCT-121

Assignment Name: Concepts in Genetics

Year: 2023

Verification Status: Verified by Professor

Attempt all questions. The marks for each question are indicated against it.

Maximum marks: 50

Part-(A)

Q1) Highlight the unique features of any two model organisms and their suitability for specific studies.

Ans) Escherichia coli is unicellular, rod shaped, flagellated, Gram negative bacteria. They don't make their own food and can live with or without oxygen. With the exception of a few strains, it doesn't make people sick and lives in the guts of many animals, including humans. Most of the time, it reproduces by a process called binary fission, and it can exchange genetic material through parasexual processes like conjugation.

The Advantages of E. Coli as a Model Organism are:

1. Multiplies very rapidly; divides every 20 min in a rich medium.

2. Can grow in both semi-solid medium and liquid broth. Pure strains are easier to find because they can multiply as single cells and form a group of cells with the same DNA, called a colony.

3. Haploid organism, useful for isolation of mutants.

4. All the genes are in a single circular chromosome with 4.64 million base pairs of DNAs. Most of the genes are single copies, and there isn't much non-coding DNA.

5. Harbours plasmids which have been modified for use in genetic engineering.

Saccharomyces cerevisiae, also known as brewer's yeast, is a single-celled eukaryote that can be either haploid or diploid. It has two types of mating, a and a;. The haploid cells of mating types that are different from each other fuse to make diploid cells. Mitosis is the process by which both haploid and diploid cells make copies of themselves by budding off copies of themselves. Through a process called meiosis, the diploid cells can change back to haploid, like when they are hungry.

The Advantages of Yeast Apart from Being Unicellular Eukaryote Include:

1. In the lab, it can be grown easily and cheaply.

2. Short life cycle (90 min).

3. All the products of meiosis, called "unordered tetrads," are kept in an ascus, which can be taken out and studied to find out where a crossover happened and to map genes.

4. There are a lot of mutants to choose from.

5. Its genome is 12 Mbp and has very little DNA that doesn't code for proteins. Foreign genes can be put into yeast by putting them into plasmids. Also, large pieces of DNA can be carried by Yeast artificial chromosomes. It is not too hard to change its genome.

Q2) Draw the Punnet square to predict the outcome of:

(i) AaBb X AaBb

Ans)

(ii) AaBbCc X AaBbCc

Ans)

Q3) Differentiate between recessive and dominant epistasis.

Ans) The main difference between dominant and recessive epistasis is that in dominant epistasis, the dominant allele of one gene hides the expression of all alleles of another gene, while in recessive epistasis, the recessive alleles of one gene hide the expression of all alleles of another gene.

Epistasis is a phenomenon or type of polygenic interaction in which one gene controls the trait of another gene that is controlled by a different gene. Both genes have an effect on how the trait looks, but the effect of one gene is hidden by the effect of the other. When epistasis is present, genes can be either dominant or recessive. So, dominant epistasis and recessive epistasis are both types of epistasis.

The genes in a person don't work separately from each other; instead, they work in the same environment. Because of this, there are interactions between genes. In epistasis, the interactions between genes are opposite. One gene blocks the expression of another gene. In dominant epistasis, the dominant allele of one gene blocks the expression of all alleles of another gene. In recessive epistasis, the recessive alleles of one gene block the expression of all alleles of another gene. So, this is the main difference between epistasis that is dominant and epistasis that is recessive.

Epistasis is a type of gene interaction in which one gene stops another gene from being expressed in its phenotypic form. The gene that hides the effect of another gene that is not an allele is called an epistatic gene. The hypostatic gene is the one that is turned off by the epistatic gene. Epistasis comes in different forms, such as dominant and recessive. In dominant epistasis, the epistatic gene is in the dominant state, and in recessive epistasis, it is in the recessive state. So, that's the difference between dominant and recessive epistasis in a nutshell.

Q4) (a) What are the limitations of cis-trans test?

Ans)

Limitations of Cis-Trans Test

1. The complementation test can be used on parts of DNA that code for a product that can be spread, but not on cis-acting sites.

2. If a mutation is recessive to wild type, the results of a trans-test are clear. In other words, the phenotype of the cis test for mutants with the same or different genes is the same as the wild type. It doesn't tell us anything about dominant mutations or traits with more than one gene whose products interact, like epistatic interactions.

3. Through "intragenic complementation," alleles of the same gene can sometimes help each other out. This can happen when the proteins in the body are oligomeric.

4. Sometimes, when two genes have different changes, they don't work well together. When two gene loci make proteins that physically interact with each other, like synaptic proteins in C. elegans, this is a rare event.

5. A polar mutation is a change in a gene that affects not only how it works but also how one or more nearby genes are expressed. These genes are located after the gene that was changed. In this case, you can't use the complementation test.

Q4) (b) Describe the Griffith’s experiment on transformation.

Ans) Frederick Griffith found that Streptococcus pneumoniae changes in 1928. It was the first time that bacteria were shown to share genes. The wild type strains of this bacterium are dangerous to mammals, and the capsular polysaccharide in them makes them form smooth, shiny colonies on agar plates. When polysaccharide synthesis is changed by mutations, bacteria colonies with a rough shape are made. These strains are not harmful. Also, there were different biochemical types of S type that were easy to tell apart immunologically. Different types of smooth can be changed to rough in different ways.

Q5) (a) Differentiate between generalised and specialised transduction.

Ans)

Generalised Transduction

1. Generalized transduction is when all the pieces of donor DNA from any part of the chromosome have a chance to get into the transducing bacteriophage.

2. In this type of transduction, the bacteriophage first takes over the donor cell and starts the lytic cycle.

3. When a virus enters a bacterial cell, it takes over the cell and makes virus parts like the genome, enzymes, capsid, head tail, and tail fibres. Then, a viral enzyme breaks up the DNA of the host cell into small pieces.

Specialised Transduction

1. In specialised transduction, bacteriophages move only a small number of restricted genes from donor bacteria to recipient bacteria. Only temperate bacteriophages that go through a lysogenic cycle in the donor cell can do specialised transduction.

2. First, temperate bacteriophages get into donor bacteria. Then, their genomes get combined with the DNA of the host cell at a certain spot, where they stay dormant and are passed from one generation to the next when the cell divides. Temperate phage is the name for a type of bacteriophage that goes through a lysogenic cycle.

3. When a chemical or UV light is shined on a lysogenic cell, for example, it causes the virus genome to be made from the genome of the host cell. This starts the lytic cycle.

Q5) (b) Distinguish independent assortment from linkage in genetic crosses.

Ans) Genes on the same chromosome can be linked in a full or partial way. Linkage is usually not complete; we only know of a few cases where it is. Independent assortment, on the other hand, happens when gene pairs are not on the same chromosome or are far apart on the same chromosome. If two genes are on the same chromosome, they are said to be syntenic. This is true whether the genes are linked or not. If the linkage is complete, a test cross for linked genes will produce only two types of offspring in equal numbers. If the linkage is not complete, however, it will produce four types of offspring in different numbers (parental>recombinants). Also, the arrangement of gene pairs determines which classes will be parental and which will be recombinants, even though the rate of recombination won't change whether the gene pairs are in cis or trans configuration. Complete linkage is rare, but Drosophila males are a good example.

 Part-(B)

Maximum marks: 50

Q1) Give an overview of development in Drosophila.

Ans) At 240C, Drosophila can go through its whole life cycle in less than two weeks. The stages are the fertilised egg, the first, second, and third in stars of the larva, and the pupa, from which the fly emerges. Each stage of a larva is bigger than the one before it. The first two instars stay inside the food, but the third instar moves out and settles on a dry surface. From now on until they get out, they don't eat anything. During pupation, the larva changes into an adult, and most of the larva's structures are destroyed. The adult fly is built piece by piece by turning on imaginal discs that were kept aside in the larva.

The egg is made in the fly's ovary, which is made up of ovarioles. At the end of an ovariole, a stem cell divides in an uneven way to make a single germ cell, which then divides four more times to make 16 cells. One of these cells finishes the process of meiosis and turns into an oocyte. The other 15 cells are nurse cells, which make proteins and RNA to feed the oocyte and send gene products that have a material effect into it. While the follicle cells make the eggshell, the oocyte grows.

Early development happens inside the egg case, and in about 24 hours, the first instar larva hatches. The first nine cell divisions in a fertilised egg happen at the same time and very quickly without dividing the cytoplasm. This makes a cluster of nuclei. The nuclei start to move toward the outside of the cell, and about ten pole cells are set aside to become the germ line. Then, the pole cells divide twice more and move back into the embryo through a process called invagination. The rest of the embryo's nuclei divide four times more, making syncytial blastoderm.

Q2) (a) Indicate two differences in sex determination mechanism between human and Drosophila.

Ans) Humans have a master switch gene called SRY (Sex determining Region on Y) on the Y chromosome. This gene controls what kind of man a man is. It makes a protein called a transcription factor, which speeds up the writing of genes on different chromosomes. This, in turn, causes the bipotential gonadal tissue to change into testes. In this way, the male pattern is put on the female pathway by default.

Q2) (b) What are the characteristic features of cytoplasmic inheritance?

Ans) The characteristic features of Cytoplasmic Inheritance are:

1. Reciprocal Differences: Characters in F1 are controlled by cytoplasmic inheritance, and there are big differences between them.

2. Maternal Effects: Because a female parent gives more cytoplasm to the zygote than a male parent, there are different maternal effects.

3. Chloroplast Genes and Mitochondrial Genes, which were very hard to map, have already been done. Some of these are the chloroplast genes in Chlamydomonas and maize and the mitochondrial genes in humans and yeast.

4. Non-Mendelian Segregation: The Mendelian inheritance shows a typical segregation pattern that is not seen in cytoplasmic inheritance.

5. Somatic Segregation: The characters, which are controlled by genes in the cytoplasm, show somatic segregation. For example, separation in somatic tissues, such as the way leaves have different colours.

6. Cytoplasmic Inheritance is controlled by DNA from the chloroplasts or the mitochondria.

Q2) (c) Write a note on histone modification.

Ans) Histones are proteins that pack DNA into chromosomes in a neat way. Changes to these proteins can turn on or off processes in the cell, such as transcription, chromosome packaging, DNA damage and repair, and chromosome packaging. The modification of histones is an important process that happens after translation and is a key part of how genes are expressed.

The changes affect the way this gene is expressed by changing the way chromatin is made or by bringing in histone modifiers. Histones pack DNA into structures called nucleosomes so that the DNA molecule can fit into the nucleus. Each of these nucleosomes is made up of two subunits. Each of these subunits is made up of the core histones H2A, H2B, H3, and H4, as well as a stabilising histone called H1.

Q3) List the characteristics of the following:

(i) Autosomal Dominant Traits

Ans) The Characteristics of Autosomal Dominant Traits:

1. A child with the problem usually has at least one parent with the problem unless it is caused by a new mutation during gametogenesis.

2. It can be passed on by either sex.

3. Men and women are both just as likely to be affected.

4. Does not skip generations unless incomplete penetrance is present.

5. When one parent is affected and the other is not, there is a 50 percent chance that the child will also be affected.

6. If the trait is fully penetrant, parents who do not have the trait do not pass it on to their children.

(ii) X-linked dominant traits

Ans) The Characteristics of an X-Linked Dominant Trait:

1. X-linked dominant traits appear in both females and males, but they are more common in females than males.

2. They don't go from one generation to the next like autosomal dominant traits do.

3. An X-linked dominant trait comes from a man's mother, and he gives it to all of his daughters.

4. On the other hand, a female gets an X-chromosome from both parents, so either parent can pass on the trait.

5. The children of a mother with the disease have a 50% chance of getting it, no matter what gender they are.

6. Each child has a parent who is hurt.

7. Females are often less affected than men, but this is not always the case. Some diseases only affect women, probably because they kill male babies in the womb.

Q4) Describe structural chromosomal aberrations.

Ans) In the end, structural chromosome aberrations are caused by broken chromosomes that come back together in a strange way. Experiments can be done to make them by exposing living cells to mutagens like ionising radiation. But mistakes in recombination can cause somatic cells and germ cells to change their structures on their own. Before meiotic recombination happens, homologous chromosomes join together through a process called synapsis. During this process, one homolog finds complementary sequences on the other homolog.

Mismatching can happen during this process, especially at sites on chromosomes where DNA sequences are repeated in tandem. This could cause the DNA at those spots to be duplicated or lost. In the same way, synapsis between homologous sites on nonhomologous chromosomes can lead to accidental recombination between nonhomologous chromosomes, which can lead to the transfer of chromosomal segments from one chromosome to another. These changes are called "translocations," and the process has been renamed "nonallelic homologous recombination." Nonhomologous end joining is another way that things can change places.

Somatic cells can also have recombination between homologous chromosomes pairing and chromatid exchange can sometimes be seen in normal chromosome preparations. But the main evidence comes from studies of DNA markers in neoplasia, in which people who are heterozygous at a number of gene loci on a pair of chromosomes have tumours that are homozygous at those loci on the same pair of chromosomes.

Analysis of the chromosomes of cell cultures that were irradiated before DNA synthesis shows that when a chromosome breaks, it makes two ends that are not stable. Most of the time, DNA repair mechanisms inside the cell make sure that the two ends are joined back together. But if there is more than one break, the correct ends may not be put back together, which can lead to abnormal chromosomes.

Q5) (a) Describe ways to analyse quantitative traits.

Ans) A group of people's quantitative qualities are measured, and numerous statistical methods are needed for their analysis. Measures of central tendency include mean, mode, variance, standard deviation, and covariance.

The distribution's centre is shown by the mean. By summing up all the individual measurements and dividing by the total number of measurements in the sample (n), it is determined as follows:

The most common observation is the mode.

The degree to which the phenotypes are clustered around the mean is shown by the variance . It determines the distribution's spread; the bigger the variance, the wider the distribution is. Two distributions with the same mean but distinct variances are conceivable. This formula is used to determine sample variance:

Where,

The square root of variance yields the standard deviation(s). It is represented using the same measurements' units.

If there is a statistically significant link between two variables, it may be determined using correlation. It illustrates prevailing patterns while tolerating deviations. A scatter diagram is created using the sample data, which is gathered as paired data. It reveals if the link is linear or non-linear at first look. The trends in a linear connection might be either upward or downward. The linear correlation coefficient, abbreviated r, is determined for accurate analysis.

Q5) (b) Explain the terms; orthologs, paralogs and xenologs.

Ans) Orthologs are sequences that are the same in different species but came from the same ancestral gene. Like human and rat myoglobin and human and bovine ribonuclease, they are thought to have similar or the same biological functions.

When a gene got copied in the same species, it made two identical sequences. These are called paralogs. For example, human alpha-1 globin and alpha-2 globin are both paralogs, and their amino acids are the same in both.

Xenologs are a type of orthologs that happen when homologous sequences are passed from one species to another horizontally. It happens a lot between bacteria, and it has even been seen between bacteria and eukaryotes and between different kingdoms of eukaryotes.