lab content

Question 1

the natural function of restriction endonucleases is in the protection of bacteria. What specific role do they play in this process?

Answer 1

Cleave the DNA of infecting viruses

Question 2

why should you perform a very brief low speed spin in a microcentrifuge after setting up your PCR?

Answer 2

to collect contents at the bottom of the tubes

Question 3

you have performed agarose gel electrophoresis of your amplified PCR product however you notice many unspecific bands on the gel. What could be the reason for this?

Answer 3

annealing temperature too low

> low annealing temperature is a common cause of nonspecific bands in PCR. When the annealing temperature is too low, the primers may bind to non-target sequences, resulting in multiple bands after electrophoresis.

Question 4

how could you most accurately pipette 384micro litres?

Answer 4

use a p1000 to pipette 384 micro litres

Question 5

in a lab report or scientific paper, where should your statistical approach be described?

Answer 5

methods

Question 6

what could a significance value of p>0.05 suggest?

Answer 6

explanatory variable did not explain significant variation in our response variable

Question 7

you are given a micropipette and asked to measure a volume of 500 micro litres. what is the equivalent of this in L?

Answer 7

0.0005L

Question 8

if the pH of your Tris-EDTA (TE) buffer is 9.57, how would you adjust the pH to the desired pH of 7.5?

Answer 8

add HCL

Question 9

you are making a solution that requires you to pipette 10 micro litres, 18 micro litres and 495 micro litres. what are the best choices of pipettes?

Answer 9

P10, P20, and P1000

Question 10

what is the hardy-weinberg equation?

Answer 10

p^2 + 2pq + q^2 = 1

p TT homozygous dominant
pq Tt heterozygous
q tt homozygous recessive

Question 11

after taking a buccal swab, the cheek cell preparation was heated to 55 degrees. why is this?

Answer 11

so that proteinase K can be most effective

Question 12

what does proteinase K do?

Answer 12

Proteinase K is commonly used in molecular biology to digest protein and remove contamination from preparations of nucleic acid. Addition of Proteinase K to nucleic acid preparations rapidly inactivates nucleases that might otherwise degrade the DNA or RNA during purification.

Question 13

what is EDTA?

Answer 13

Ethylenediaminetetraacetic acid (EDTA) is a medication used in the management and treatment of heavy metal toxicity. It is in the chelating class of drugs. This activity outlines and reviews the indications, actions, and contraindications for EDTA as a valuable agent in managing lead toxicity

Question 14

The buccal swab was placed in lysis buffer that contains detergent and a chelating agent known as EDTA.
what is the role of the detergent and the chelating agent?

Answer 14

detergent; break cell membrane
chelating agent; stop the DNA from being broken down by DNAses

Question 15

During DNA extraction, you used a mini-column assembly that is packaged with silica. what is the role of the silica in this procedure?

Answer 15

to trap the DNA into the column

Question 16

what is the purpose of the TE buffer added at the end of DNA extraction?

Answer 16

to keep the DNA from degrading and store it well

Question 17

what is 5ng in ug?

Answer 17

0.005

Question 18

1ng in g?

Answer 18

0.000000001

Question 19

The concentration of double-stranded DNA can be calculated from the equation: DNA concentration in ng/µl = A260 x 50 ng/µl x dilution factor. You add 1µl of purified DNA to 4µl of distilled water then measure the absorbance of this diluted sample at 260nm to be 0.525. What is the concentration of DNA in the stock solution?

Answer 19

Absorbance = 0.525
dilution factor = total volume/volume of DNA
= (4+1)/5 =5

DNAconcentrationinng/µl=A 260 ×50ng/µl×dilutionfactor

=0.525x50x5
=131.25ng/ul

ng/ul to ug/ul…. divide by 1000
= 0.131ug/ul

Question 20

following a PCR reaction you obtain the following readings from the Nanodrop machine: A260=0.845;A280-0.446.
what is the A260/A280 ratio of the purified DNA?

Answer 20

0.845/0.446 = 1.89

Question 21

is it true that provided the number of base pairs is a multiple of three, insertion of additional DNA in the coding region of a protein is unlikely to have a dramatic effect on protein function?

Answer 21

no, false.
could still have a significant effect on protein function

Question 22

what DNA sequence might be recognised by a restriction endonuclease?

Answer 22

AAGCTT

Question 23

discuss restriction endonucleases

Answer 23

also known as restriction enzymes, are enzymes that cut DNA at specific sequences, typically recognising short palindromic sequences (usually 4-8 base pairs in length).
they are widely used in molecular biology for gene cloning, DNA analysis, and genetic engineering.

recognises GAATTC (cuts between G and A
AAGCTT
GGATCC
CCCGGG
CTGCAG
GCGGCCGC
AGCT

Question 24

when searching a query sequence within the NCBI database, give an example of a correct statement?

Answer 24

translated nucleotide query against protein database done by blastx

Question 25

In a comparison of two DNA sequences found in the same location on homologous chromosomes, one of the homologues carries the sequence 5’AACTACGA-3’ and the other homologue carries the sequence 5’AACTTCGA3’.
Within a population you discover that each of these sequences is common.
What describes these sequences?

Answer 25

they contain a SNP that may be useful for genetic mapping

Question 26

what is the number of dominant alleles in a population of 100 individuals with the following genotypes: 30BB, 60 Bb, 10bb?

Answer 26

BB: 30
Bb: 60
bb: 10

BB (2 B alleles)
= 30 x 2 = 60

Bb (1 B allele)
= 60 x 1 = 60

bb (0 B alleles)
= 10 x 0 = 0

=> 60 + 60 =120

Question 27

what are some statements regarding single nucleotide polymorphisms (SNPs)?

Answer 27

they can change effectiveness of drugs between individuals

they have to occur in a significant fraction of the population (e.g. >1%)

Question 28

if your A260/A280 ratio is 1.85, what does this tell you about your DNA sample?

Answer 28

you have a reliable DNA preparation.

this ratio is commonly used to assess the purity of DNA samples as it indicates the presence of protein or other contaminants that might affect downstream applications.

1.8-2.0 = pure DNA samples (ratios closer to 2.0 can indicate RNA contamination)

below 1.8 is protein or phenol contamination

Question 29

if your DNA conc. is 0.59 ug/ul what colume would you require to obtain 25ug?

Answer 29

42.4ul

volume= amount needed/conc.

25/0.59= 42.37ul