Bio 423 Final Exam Questions

By Semra Kocabiyik 1. What are phagemids? And what are the possible uses of them? And what are the essential components of a contemporary phagemid? Explain the functions.

Phagemid A phagemid is a type of cloning genetics vector developed as a co-infection of the M13 helper phage and plasmids to produce a smaller version of the virus. an example is PRS314 which is of 4.78 kb size They find their application at phage displays. A phagemid is different than a closely related cloning vector called a cosmid. While a cosmid can enter a host cell very effectively, almost all of the viral genes have been removed to make room for exoginous DNA, therefore the virus cannot replicate itself. In a phagemid, however, an origin of replication is present. This means that in the presence of a 'helper' virus such as f1, the rest of the genes to replicate viral proteins are present, therefore more virus particles can be created using the host cells resources.

Phage display Phage display is a test to screen for protein interactions by integrating multiple genes from a gene bank into phage. Like the two-hybrid system, phage display is used for the high-throughput screening of protein interactions. The principle of this method is summarized as follows: 1. The function of protein X is unknown. The protein is used to coat the surface of a small plastic dish. 2. Numerous genes, often all the genes in an organism's genome, are expressed in a library as fusions with the coat protein of a bacteriophage, so that they are displayed on the surface of the viral particle. 3. This phage-display library is added to the dish. After a while, the dish is washed. 4. Phage-displaying proteins that interact with protein X remain attached to the dish, while all others are washed away. DNA extracted from interacting phage contains the sequences of interacting proteins. A phage will target another phagemid and insert its DNA between the signal and the native DNA, the result of this foreign DNA causes the phagemid to secrete a specific amino acid sequence coding for the foreign DNA. from: The Wellcome Trust Phage display is also a widely used method for in vitro protein evolution (also called protein

engineering). Competing methods for in vitro protein evolution are yeast display, bacterial display, ribosome display, and mRNA display.

2. Describe a way to obtain a full size cDNA from the RNA isolation stage 3. What are the basic features of high throughput DNA sequencing machines? 4. How do you make use of DNA microarray technology to detect single nucleotide polymorphisms (SNPs) on the exon of a gene?