PCR and microbiomes

Question 1

steps of the PCR thermocycler program

Answer 1

1. Denaturation
2. Annealing
3. Elongation

Question 2

how to calculate the number of copies of a given amplification

Answer 2

grows exponentally

Question 3

essential components in the reaction mixture

Answer 3

1. primer-(FV)(FC)=(SC)(X)
2. buffer- (FC)(FV)=(SC)(X)
3. NTPs- same as 5
4. polymerase-same as 5
5. template DNA-fix measurements and repeat 1
6. water- added volumes-FV

Question 4

main considerations for designing PCR primers

Answer 4

denaturing heat and where it cuts the gene so not to lose some of it.

Question 5

how to use PCR to introduce point mutations and restriction sites into a gene

Answer 5

primers designed to be come restriction sites or promoters

Question 6

the applications of PCR

Answer 6

forensics
evaluate cancers
ID specific alleles 
Detection of infectious agents
studying evolution

Question 7

determination of the Random Match probability.

Answer 7

multiply the probabilities together

Question 8

VNTR

Answer 8

variable number tandem repeat (or VNTR) is a location in a genome where a short nucleotide sequence is organized as a tandem repeat.

Question 9

STR

Answer 9

Short Tandem Repeats (STRs): regions in the genome where short stretches of sequences are repeated. The number of repeats can vary per individual.

Question 10

RFLPs

Answer 10

Restriction Fragment Length Polymorphisms (RFLPs) – amplify regions of DNA with a known restriction site

Question 11

troubleshoot issues with PCR reactions

Answer 11

possibility of errors and those errors repeat in those copies

Question 12

the basic set up of a Chip

Answer 12

sticky pieces that the DNA can attach to and will light up in the color given to it, there a some spots set to always light up

Question 13

differences between DNA and RNA-based arrays

Answer 13

Identifying which genes are being expressed (RNA). DNA looks at the whole genome.

Question 14

Comparative Genomics

Answer 14

a field of biological research in which the genomic features of different organisms are compared.

Question 15

Data Mining

Answer 15

“the nontrivial extraction of implicit, previously unknown, and potentially useful information from data”

Question 16

Phenomic

Answer 16

The Phenotypes that result from the genome and the proteome

Question 17

Proteomics

Answer 17

Identification of all the proteins expressed in every cell of an organism

Question 18

Transcriptomics

Answer 18

the study of the transcriptome—the complete set of RNA transcripts that are produced by the genome

Question 19

Bioinformatics

Answer 19

the use of computer programs to find things like homologs and primers

Question 20

Mapping

Answer 20

Mapping revealed that genes are not evenly dispersed through the genome, but are clustered

Question 21

Annotation

Answer 21

the process of identifying regions in the sequence

Question 22

Molecular Clocks

Answer 22

a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged

Question 23

Housekeeping genes

Answer 23

typically constitutive genes that are required for the maintenance of basic cellular function, and are expressed in all cells

Question 24

Neutral regions

Answer 24

DNA segments without active roles in the cell will be a reflection of the frequency of random mutation

Question 25

Northern blots

Answer 25

mRNA is isolated from a tissue and run on an Agarose gel
The mRNA fragments are transferred from the gel to a 2-D membrane.
The membrane is incubated with a labeled DNA probe that will hybridize to the mRNA that contains its complementary sequence.

Question 26

Microbiome

Answer 26

comprises all of the genetic material with a Microbiotia

Question 27

Microbiotia

Answer 27

the entire collection of microorganisms in a specific niche

Question 28

Amplicon sequencing

Answer 28

amplify a highly conserved gene (eg 16S rRNA) to get sequence for all of the different bacteria in the microbiota.

Question 29

Metagenomic sequencing

Answer 29

no amplification, just isolate DNA and start sequencing

Question 30

denaturing

Answer 30

the Double-stranded DNA template must be melted apart to 2 single strands.

Question 31

annealing

Answer 31

the Primers have to base-pair with the complementary DNA on the template

Question 32

elongation

Answer 32

Initiation – The initial reaction is heated for several minutes to destroy any other enzymes in the reaction mix.
Final elongation – after the last cycle, the reaction is held at the elongation temperature to let any incomplete fragments finish

Question 33

southern blot

Answer 33

Use nucleases to cut up the genomic DNA into smaller fragments.
Separate the fragments by size on an agarose gel
Transfer the DNA fragments from the gel to a 2-D membrane.
Incubate with a labeled DNA probe that will hybridize to the fragment of DNA that contains its complementary sequence.