Gen 604 based on HW#13

Suppose you have identified a mutation in a single gene that is responsible for a disease.Because the molecular basis for this disease is so simple, gene therapy, where the mutant gene is replaced by the correct version using retroviral vectors, might be an option to treat the disease. Describe how viral gene delivery systems of this sort are often difficult to make work

1) Integration of the retroviral gene of interest can only happen when cells are actively dividing. Normally however, few cells in the body are actively dividing. 2) In addition viruses of this sort can cause acute immune responses that can be worse than the condition one is trying to treat. 3) The insertion of a gene into the genome can occur within another gene, effectively causing another mutation. 4)There is even the chance that the attenuated retrovirus used to deliver the gene of interest could recombine with a virus already present in the host cell, creating a new virus

. The human genome project has revealed that the human genome is comprised of ____ % transposable elements and ____ % coding sequence.

50, 2

ASO analyses:

Allele-specific oligonucleotide analyses use PCR to identify patients with a specific mutation. In ASO, PCR primers designed to bind to specific mutations found only in disease alleles are used on a patient's DNA. Ologonucleotide probes are hybridized to patient sample DNA and PCR products will be amplified only if the patient has the mutant allele.

Gene Expression Microarrays are useful in transcriptomics. Describe an experiment using gene expression microarrays to identify genes involved lung cancer. For your experiment, you have 10 samples each of normal and cancerous lung tissue and a microarray containing all human genes.

Extract mRNA from each of the tissues. Use the mRNA from each sample to make labeled cDNA probes. The probes from each sample type will have a different label, say red for cancerous and green for normal. Mix equal amounts of labeled cDNA from normal and cancerous lungs and hybridize the mixture to a microarray containing all human genes. Genes that are expressed equally in both samples will be detected as yellow (half red-half green). Genes that areupregulated in cancer will be detected as red and those upregulated in normal tissues will be green. The putative cancer genes are those that are detected as red.

Describe how gene duplication can give rise to multi-gene families over the course ofevolution.

Gene duplications are rare but when they occur, the gene copies that are produced often accumulate mutations, causing each gene to have different sequences and eventually different functions. This duplication and divergence can proceed over the course of millions of years to give rise to a multi-gene family.

Describe one example of a genetically engineered plant. Include a description of the gene or genes that were incorporated into the plant.

Glyphosate-resistant plants were engineered to express the bacterial EPSP synthase gene. This gene gives resistance to the herbicide Roundup or glyphosate. or Golden Rice was genetically engineered to produce beta-carotene, a precursor to vitamin A. Three genes involved in beta-carotene synthesis were transferred into the rice genome.

Orthology:

Homologous genes from different species thought to have descended from a common ancestor are called orthologs. Orthologs derive from speciation events.

Paralogy:

Homologous genes in the same species are called paralogs. Paralogs derive from gene duplication events.

Describe in general terms how known sequence elements, such as the TATA box in promoters, are used by computational algorithms to annotate genomes.

Known sequence elements such as the TATA box, intron/exon boundaries, start codons, stop codons and others are searched for in DNA sequence data and used to Infer open reading frames and gene structure.

Describe one application of recombinant DNA technology in vaccine production.

Recombinant DNA technology can be used to express proteins that can be used as subunit vaccines. Subunit vaccines consist of one or more of the small surface proteins found on the virus capsid. Injection of the purified proteins can stimulate an immune responses and protect the injected person from the virus. Subunit vaccines for Hepatitis B virus are in use.

RFLP analyses:

Restriction fragment length polymorphism analyses use restriction enzymes to detect mutations associated with disease. When mutations occur at specific restriction sites, they can be detected using a Southern blot.

How can BLAST searches for homologous genes tell us about the function of a DNA sequence from a gene with unknown function?

Searching databases of gene sequences like GenBank using BLAST can identify genes that are homologous to the unknown gene. In many cases the function of these homologous genes will be known. The gene of interest will likely share the same function as the homologous genes with known function.

What is an open reading frame?

Sequences of triplet nucleotides that, after transcription and mRNA splicing, are translated into the amino acid sequence of a protein.

. Comparative genomics has revealed that the genomes of humans and chimpanzees are 98% identical. This was an unexpected finding considering that humans and chimps are so morphologically different. Describe one way in which small differences between the human and chimp genomes can give rise to such pronounced morphological differences.

The 2% difference in the genomes of humans and chimps could be focused on short regulatory regions in the genome. Humans and chimps are not so different in terms of sequence, but they are very different in terms of how and when genes are expressed.

What is one drawback of RFLP analysis?

The mutation of interest must occur within a restriction site in order to be an effective means of screening. Because restriction sites are relatively rare, the RFLP method will be unable to detect many mutations because they do not affect a restriction site.

Prior to the human genome project, scientists had hypothesized that the human genome contained between 80,000 and 100,000 genes. Roughly how many genes does the human genome contain? What explains the discrepancy between the hypothesized and observed gene count? T

There are 20,000 genes in the human genome. Most of the transcripts are spliced in to yield 2 or more kinds or mRNAs, dramatically increasing the number of gene products (proteins) that can be expressed from a given gene.