Quiz 4-Genetic linkage mapping and techniques

Linked Genes

Genes located on the same chromosome are called linked genes. They are physically linked and do not assort independently. recombinant frequency is less than 50%-genes are linked.

Parental vs. Recombinant Chromosomes

Parental chromosomes carry the original combinations of alleles from the parents, while recombinant chromosomes have undergone crossing over, resulting in new allele combinations not found in the parental chromosomes.

Explain how a recombinant gamete can be produced by independent assortment and by homologous recombination.

A recombinant gamete can be produced by independent assortment when genes on different chromosomes segregate independently during meiosis, leading to new combinations of alleles. Additionally, homologous recombination occurs during meiosis, where adjacent homologous chromosomes exchange segments, resulting in recombinant chromosomes with new allele combinations.

Describe a chromosome map and describe how a chromosome map (i.e. linkage map) is generated.

A chromosome map, specifically a  linkage map (or genetic map), is a diagram representation showing the linear order of genes or genetic markers and their relative distances along a chromosome.  linkage map is based on recombination frequencies calculated from the patterns of inheritance during meiosis

Describe a single nucleotide polymorphism (SNP) and explain how a SNP can create a restriction fragment length polymorphism (RFLP).

Single Nucleotide Polymorphism (SNP): A change in a single nucleotide but typically in non-coding regions of the genome.

Restriction Fragment Length Polymorphism (RFLP): Created when a SNP occurs at a restriction site, destroying or creating a binding site for a restriction enzyme (e.g., EcoRI). This changes the resulting DNA fragment pattern on a gel

PCR? and how does this amplify DNA?

PCR amplifies a specific region of DNA by exploiting the natural mechanism of DNA replication and applying it through three core, repeated steps: Denaturing at 95 degrees, then Annealing 55 degrees, then Elonggation at 72 degrees.
The double stranded DNA is seperated into single strands and then cooled so that primers can bind to complementary base pairings on single strands- these flank (surround regions) the region of DNA intended to amplify. The heat stable Taq DNA poly. adds neucleotides to primers and synthesizes DNA complementary to the templete strand.

compoenets of a PCR: template, ploymerase, primer, dNTPs, Buffer

Describe a dideoxynucleotide (ddNTP)

A dideoxynucleotide (ddNTP) is a modified DNA nucleotide lacking the 3′-hydroxyl (−OH group required for DNA chain elongation. Due to this missing (−OH) group, ddNTPs act as chain terminators, stopping DNA replication when incorporated by DNA polymerase. They are used in Sanger sequencing to create fragments of varying lengths that reveal the DNA sequence.

explain how ddNTPs are used in the dideoxy method of DNA sequencing.

1. Reaction Setup: A sequencing reaction includes the target DNA template, DNA polymerase, primer, a large amount of normal dNTPs (A, T, C, G), and a small amount of fluorescently labeled ddNTPs.

2. Chain Termination: As DNA polymerase builds a new DNA strand, it usually adds dNTPs. Occasionally, it will randomly add a ddNTP instead of a dNTP. When this happens, polymerization stops.

3. Fragment Generation: Because this occurs randomly across millions of molecules, the reaction generates a mixture of DNA fragments of every possible length, each ending with a labeled ddNTP.

4. Separation and Detection: The fragments are separated by size using capillary electrophoresis. Because each base (A, T, C, G) has a unique fluorescent color, a detector identifies the terminal base of each fragment in order of length, translating this into the DNA sequence.

the absence of the 3′-OH group on ddNTPs turns them into "stop signs" that allow researchers to pinpoint the precise location of each nucleotide.

Whole genome sequencing vs whole exome

Whole Genome: Sequences the entire DNA of an organism, including coding and non-coding regions.

Whole Exome: Specifically targets and sequences only the protein-coding regions (exons), which requires a "filtering" or enrichment step

types of gene therapy, including the types of target cells and how components are delivered to cells.

CRISPR-Cas9 is a precise gene-editing technology using a guide RNA to direct to cut specific DNA sequences. It enables somatic therapies (targeting non-reproductive cells, e.g., blood, liver) for treating individuals and germline therapies (targeting embryos/gametes) for heritable changes-reducing the chance of bad genes being passed onto next generation.

 Delivery is achieved via viral vectors, mRNA, or physical methods-eg: ex vivo cell engineering.