Exam 2 Study Guide Flashcards
What are the basic physiological characteristics of the gram stain?
Purple coloring indicates gram positive cells
Pink coloring indicates gram negative cells
What are the basic physiological characteristics of the catalase test
Bubbling when gas is released
What are the basic physiological characteristics of the glucose fermentation test
Yellow coloring indicates acid formation from glucose fermentation
What are the basic physiological characteristics of the nitrate reduction test
Pink or red medium color change indicates presence of nitrite
Gas indicates denitrification went beyond nitrite to nitrogen gas
What are the basic physiological characteristics of the oxidase test?
Presence of oxygen changes strip to dark blue color
What are the basic physiological characteristics of the motility test?
Cloudiness means cells likely motile
Line of growth means cells not motile
What are the basic physiological characteristics of the thioglycolate test?
Oxygen abundant at top of agar, with decreasing amounts going deeper into the agar
Pink or red in the oxidized state and colorless when reduced
What is the function of ExoSAP-IT? When is it used?
Enzyme mix that ensures only PCR product remains for subsequent processes
Used after gel electrophoresis
What is the function of BigDye?
Specialized sequencing chemistry that enables the incorporation of fluorescently labeled ddNTPs during Sanger sequencing to allow the detection and analysis of DNA sequences with accuracy
What is the function of CleanSeq and when is it used?
Used to clean up PCR product after gel electrophoresis PCR analysis
What information is looked for on the agarose gel of our sample?
gel electrophoesis separates DNA fragments by size
- smaller fragments move more quickly through the gel than larger fragments
What is dideoxy sequencing and how does it work?
Sanger sequencing
- It relies on the termination of DNA synthesis at specific positions, allowing for the determination of the sequence by identifying the terminated fragments
Explain the BLAST process and significance
BLAST searches through vast library of information, given a sequence of genetic code
- finds similarities, helps understand genes and proteins, track evolution, medical uses, easily search through databases
What is the E value?
E-value tells you the probability of getting a match between your query sequence and a sequence in the database by random chance. A lower E-value indicates a more significant or meaningful match
What does the percent identity number tell us?
indicates the similarity between two sequences by measuring the proportion of identical positions (nucleotides or amino acids) between them
