Bcmb 406b - Study guides, Class notes & Summaries

Lab 1 - Exercise 1: Primer Analysis and PCR Trouble-Shooting - Answer Compared and contrasted two primer pairs to find the qualities that contribute to the likelihood of a given primer pair producing the desired product. - NetPrimer Lab 1 - Exercise 2: Primer Design from a Target Sequence - Answer 1. Nucleotide BLAST (BlastN): identify the sequence. --> indicate organism of origin, size of assigned DNA sequence, and the name of the protein it encodes.

______ methodology allows for the study of complex *cellular regulation of genes *the role of specific amino acid residues in protein structure, catalytic function and ligand binding capacity *mechanisms involved in infectious and genetic disease - Answer Site directed mutagenesis

What is the most important factor in a successful PCR reaction? - Well designed primers What can the theory of primer design also be applied to? - The use of oligonucleotides in other techniques that utilize annealing or formations of duplexes of nucleotides (probes in Southern blot, Northern Blot, ect.) What variables influence the success of a PCR reaction? - - quality of template DNA - cycling conditions (melting temp., duration) - specificity and stability of the PCR primers What ...

PCR allows for: - amplification of minute amounts of template DNA can generate thousands or millions of copies of that sequence What is one of the most important parameters for a successful PCR? - well designed primers Name 3 variables that influence the success of a PCR reaction - 1. quality of template DNA 2. cycling conditions 3. specificity and stability of PCR primers The target sequence determines what criteria in primer design for PCR? - 1. primer length 2. % GC content 3. m...

The success of a PCR reaction is mostly dependent on what? Answer> well designed primers Primer design can also be applied to what? Answer> - probes in Southern and Northern blots - DNA sequencing - microarray design What else can affect the success of a PCR reaction? Answer> - Quality of the template DNA - cycling conditions - Specificity and stability of the PCR primers What are key criteria in primer design? Answer> - Primer length - Percent GC content - Melting temper...

What describes a well defined PCR reaction? - Answer - template DNA is added in purified form - typically starts with 10^5 - 10^6 molecules of template DNA What are essential components to site directed mutagenesis? - Answer - DNA template - Primers - dNTPs - DNA polymerase

Glycoside hydrolases Answer> Hydrolyze the glycosidic bond between 2 or more carbohydrates or carbohydrate-protein bonds Carbohydrate Binding Modules Answer> - Amino acid sequence within a carbohydrate-active enzyme with a discreet fold that has carbohydrate binding activity - Maintains the interaction of the enzyme with its substrate Vector NTI Advance Answer> - Allows you to plan your experiment and ensure that it results in the desired product Benefits of in silico Answ...

The success of a PCR reaction is mostly dependent on what? - well designed primers Primer design can also be applied to what? - - probes in Southern and Northern blots - DNA sequencing - microarray design What else can affect the success of a PCR reaction? - - Quality of the template DNA - cycling conditions - Specificity and stability of the PCR primers What are key criteria in primer design? - - Primer length - Percent GC content - Melting temperature - Sequence How are Primer...

Purpose of SDS-NaOH and Sodium Acetate in Alkaline lysis method? - Answer SDS- NaOH: achieves cell lysis - Chromosomal DNA remains in a high molecular weight form but is fully denatured Sodium Acetate Solution: neutralizes solution - Chromosomal DNA randomly base pairs and becomes insoluble - High salt concentration precipitates SDS-protein complexes and high molecular weight DNA

Glycoside hydrolases - Hydrolyze the glycosidic bond between 2 or more carbohydrates or carbohydrate-protein bonds Carbohydrate Binding Modules - - Amino acid sequence within a carbohydrate-active enzyme with a discreet fold that has carbohydrate binding activity - Maintains the interaction of the enzyme with its substrate Vector NTI Advance - - Allows you to plan your experiment and ensure that it results in the desired product Benefits of in silico - - Predicts restriction fragment s...