Q1/ For a given double stranded DNA, how many reading frame are there ?

6

Q2/ In a given DNA sequence, how many open reading frames are there?

 depends on the presence of start and stop codon.

Q3/ Which of the following reading frames is an open reading frame?

 start with atg and end with taa

Q4/ You used the same primers and the same quantitative reverse transcriptase PCR
protocol for detecting the load of a retrovirus in 4 patients (…) samples ?

 A>B=C>D

Q5/ Which of the following statements is false while comparing natural replication and
polymerase chain reaction (PCR)?

 Both occur at constant temperature.

Q6/ Which of the following PCR properties change with polymerase fidelity ?

 All of the above (annealing temp, extension rate, errors/base).

Q7/ The primer melting temperature is a function of?

 all of the above (primer sequence, PCR polymerase, salt concentration)

Q8/ In order to quantitatively detect a retrovirus for overs 10 000 samples, which of the
following will you use ?

Low + reverse

Q9/ Of the following 4 primers with corresponding GC% and delta G, which one would be
the best to use ?

 GC% 50%, -0.25

Q10/ True or false: for sequencing we should use low-fidelity polymerase?

 false

Q11/ What is the function of primers in PCR?

 both A and B (help polymerase with replication, define start and end of replication)

Q12/ You design primers to detect if M.tuberculosis in one particular sample contains a
genetic mutation, that make it resistance to antibio (using sequencing). Then you have to
design primers to clone the mutant polymerases in a gene. What would you change between
the 2 PCRs ?

 Primers and DNA poly

Q13/ We design primers for gibson assembly as shown in the figure. We first design short
primers 1,2,3 and 4 that bind to the insert and backbone. Then we combine the primers
together to design the combined primers 5,6,7 and 8 for Gibson assembly. Which primers do
we use to calculate the annealing temp ?

1, 2, 3, 4

Q14/ We design primers blabla: secondary structures ?

 5,6,7 and 8.

Q15/ Where would you plae your gene for optimal expression?
3

Q16/ In blue white screening, what do blue colonies represent?

 Cells with empty plasmid vectors

Q17/ The reverse transcriptase step is required for cloning genes from which of the following
sources? 1. Bacteria 2. Retrovirus 3. Human BRCA1 gene ?

 2 only

Q18/ Which of the following determine the choice of plasmid for a cloning? 1. Host 2.
Application: cloning or expression

 1 and 2 both

Q19/ Which of the following is determined by the origin of replication of a plasmid?

 Plasmid copy number

Q20/ If a meganuclease cuts a unique 18 basepair sequence, how many meganucleases will
be have to screen to find on hat cuts our sequence of interest?

 4^18

Q21/ A new CRISPR system has been discovered with a PAM sequence of NNGG. What is the
probability of finding the PAM sequence?

 1/16

Q22/ What is NOT true about the guide RNA?

 gRNA contains the PAM

Q23/ What is the function of Cas 9 binding to the PAM?

 Binding of PAM releases energy for initiation of dna unwinding

Q24/ What is the advantage of having double guide RNAs?

 Having double guide rnas decreases off target activity

Q25/ You wish to delete the gene in pink. You have found 4 guide RNAs with the following
on-target scores (assume a higher on target is better). Assume that the off-target score for
all the gRNAs is the same. Which grna will you use?
gRNA 1: 75
gRNA 2: 60
gRNA 3: 75
gRNA 4: 60

 Either grna 1 or 3

Q26/ Now you wish to introduce a mutation at the point market with an X in the pink gene.
You have found 4 guinde RNAs with the following on target scores (higher on target is
better). Assume that the off-target score for all the gRNAs is the same. Assume gRNA 1 and 2
have the same distance from the mutation. Which gRNA will you use:
gRNA 1: 75
gRNA 2: 60
gRNA 3: 75
gRNA 4: 60

 Grna 1 only

Q27/ In order to detect an antibiotic resistance mutation in a gene, which of the following
technique will you use?

 PCR followed by sanger sequencing

Q28/ When setting up a sanger sequencing reaction each reaction should include template
DNA, nucleotides, dideoxynucleotides, buffer, DNA poly, and____?

 Forward or reverse primer (sanger run with a single primer)

Q29/ What is the sequence associated with the following gel prepared after the chain
termination Sanger experiment?
 5’- TCCT …3’

Q30/ You designed 2 primers to detect the presence of a virus in a patient sample. What
genomes will you blast the primer against?

 Virus genome

The next 8 questions are based on a blenching exercise using the files ORF gb. You will find
this gene in moodle  genetic  tests. You will need to upload the gene on benchling. The
questions are based on blast and primer design.

Q31/ Which of the annotated reading frames is an ORF ?

2

Q32/ What gene does the ORD code?

 CRP prot
Q33/ là haut

 primer pair 3

Q34/ What is the annealing temperature for the chosen pair of primers for the above
question. Remember to chose the correct poly.

 65
Q35/

?

Q36/ What is the annealing temp for the chosen pair of primers for the above question. ETC

?

Q37/ ON VERRA À L’EXAM POUR 37-38

Q39/ The next 5 questions are based on BLAST and cloning of the gene1 gb. Find it on
moodle.
What function does gene1.gb code for?

 rpsL (ribosome subunit)

Q40/ If you wish to clone the enzyme using restriction digestion, which of the following
enzyme can you use?
 HindIII

Q41/ You have to clone the gene obly for maintenance and not expression. Which of the
following vectors and strategies will you use?

 2e lien (puc 19)

Q42/ You have to clone the gene for expression. Which of the following vectores and
strategies can you use?

 both 1 and 3

Q43/ You have to clone the gene for expression of the gene with a tag. Which of the
following vectors and strategies can you use?

 rep 1 (tag au niveau de l’insert)

Q44/ the next 5 questions are based on blast and gRNA design, you work on gene2gb. What
is the gene Gene2.gb?

 actin beta gene

Q45/ Match the PAM in the correct order of the following spacers. You have to match each
spacer to its PAM Seq.
?

Q46 etc pas trouvé