Gel Electrophoresis: Visualize Question 3: Great job!

For which enzyme are

nucleotides the substrate?
and separate nucleic acids
DNA polymerase
Ligase
Question 1: What is the function of a ladder
Ribosome
in gel electrophoresis?
Protease
Gauge the size of the bands in the
sample
Question 4: Great job! What is the template
Prevent the bands from running off the gel
of the PCR reaction?
Positive control
DNA
Negative control
RNA
Proteins
Question 2: Where on the gel will the largest
Nucleotides
DNA molecules be, and why?
Near the top because they cannot
Question 5: We are going to use the blood
migrate through the matrix of the gel as
sample you collected at the crime scene.
fast
What needs to happen before the blood
Near the bottom because they carry more
sample can be used for PCR?
negative charge
DNA has to be isolated from the cells
Near the bottom because the migrate
The blood has to be frozen
through the matrix of the gel faster
No action is needed
Near the top because they are less
The tube has to be shaken
negatively charged
Question 6: What do you need to do each
Question 3: How are DNA or RNA molecules
time before using a pipette to collect liquid?
visualized on the gel?
Put on anew, sterile pipette tip
A labeled dye that binds to the DNA is
Polish the pipette
added
Shake the pipette
The DNA is extracted from the gel and then
Put on a used pipette tip
measured
The bands cast a shadow when light passes
Question 7: Great that you throw away the
through the gel
used pipette tip. Why is it important to
The negative charge of the DNA is used to
change the pipette tip?
detect the bands
To avoid cross contamination
To keep the lab assistant happy
To employ more garbage men
Polymerase Chain Reaction To keep the lab bench clean

Question 1: Great job! What is the function of Question 8: How did you collect liquid in the
primers in a PCR reaction? lab?
Bind specific sites on the DNA Using a pipette
Denature DNA Grabbing it with my hands
Bind random sites on the DNA Using a measuring cup
Copy DNA Pouring from the bottle

Question 2: Great job! What does a DNA Question 9: At this step in the PCR process,
polymerase do? what happens to the DNA?
Synthesizes DNA It will be separated into two strands
Degrades proteins It will be twisted into a double helix
Unfolds DNA It will be broken into many pieces
Cleaves DNA It is kept intact
Question 10: How is the DNA separated into different creating a specific DNA profile.
single strands? When using one primer pair in different
The high temperature (95°C) individuals, which phrase describes the PCR
The primers separate the two DNA strands product?
The DNA polymerase separates the two DNA Different length may be found in each
strands individual
The low temperature (54°C) Random sequences
Identical DNA sequences in all individuals
Question 11: What is the step in the PCR Equal length will always be found in all
reaction that is now shown called? individuals
Annealing
Denaturation Question 17: What happens to the probability
Copying of a 100% match between two different
Extension individuals when using 13 sets of primers for
the DNA profile instead of one?
Question 12: The area where the primers It decreases
bind marks which part of the PCR product? It results in a match
Beginning, 5'5 prime-end It is not affected
End, 5'5 prime-end It increases
Beginning, 3'3 prime-end
End, 3'3 prime-end Question 18: How many copies of DNA are
required to see bands on the electrophoresis
Question 13: The PCR products get a certain gel?
length due to which fact? Millions of copies
The placement of the primers 10 copies
The heat in the PCR machine 1000 copies
The DNA breaking off None
The DNA polymerase falling off
Question 19: Which word describes the
Question 14: How does the DNA polymerase charge of the DNA?
extend the primers into a new DNA strand? Negatively charged
Adding nucleotides to the 3' end of the Highly charged
primers Not charged
Adding nucleotides to the 3’ and 5' ends of Positively charged
the primers
Adding nucleotides to the 5' end of the Question 20: DNA is negatively charged. To
primers which location in the electrophoresis gel
Adding more primers to the strand does it migrate?
Positive pole
Question 15: Primers are always designed to Corners
be complementary to the template DNA Sides
strand. Which Negative pole
of these sequences is the complementary
sequence to the template sequence 5'5 Question 21: What are the building blocks of
prime-GTGGTCTGATCAACGGTAA- 3'3 prime? new copies of DNA?
3'-CACCAGACTAGTTGCCATT-5' Nucleotides
3'-GTGGTCTGATCAACGGTAA-5' Polymerase
5'-GTGGTCTGATCAACGGTAA-3' Amino acids
5'-CACCAGACTAGTTGCCATT-3' Primers

Question 16: The number of repeats of each Question 22: What is the function of primers
individual's tandem repeated regions can be in a PCR reaction?
They bind specific sites on the template 100
DNA to initiate and direct DNA None
synthesis
To separate double stranded DNA in order to Question 29: What is the purpose of PCR?
initiate and direct DNA synthesis To copy and then make many copies of
They bind random stretches of DNA to a specific region of DNA
initiate and direct DNA synthesis To reveal the sequence of a piece of DNA
Their only function is to bind DNA and they To make few copies of DNA
do not direct DNA synthesis To copy the entire human genome

Question 23: What would happen if no Question 30: Why is a PCR cycle repeated 30
polymerase was added to the PCR reaction? times?
New DNA would not be generated To get enough DNA
The primers would anneal to the DNA To avoid adding new reagents every cycle
50% less DNA would be produced To allow the polymerase to work
New DNA would contain many errors To make sure the PCR machine is working

Question 24: Which reagent acts as a Question 31: What can a DNA ladder help
template for the DNA polymerase, so it determine?
knows which new DNA to make? The length of a fragment
DNA from a blood sample The origin of the DNA
Proteins in the blood cells The DNA sequence of a fragment
Primers If DNA binds protein
Nucleotides
Question 32: Why is it possible to distinguish
Question 25: DNA polymerase binds to the individuals by running these PCR products on
template DNA. In which direction is the new a gel?
DNA subsequently synthesized? The PCR products are different lengths
5’→3’ The PCR products have different sequences
Random The PCR products have the same sequence
3'→5' The PCR products are the same length
5'→3' and 3'→5'

Question 26: Why is the Taq-polymerase SDS-PAGE: Separating proteins

special compared to most other
by molecular weight
polymerases?
It can resist high temperatures
Question 1: Why do you think we call the
It unfolds DNA
tumor-suppressing protein "p53"?
It can resist low temperatures
The molecular weight of the protein is
It synthesizes DNA
approximately 53kDa
Scientists found the exact molecular weight
Question 27: What can contamination of
of p53 after 53 attempts of electrophoresis
reagents leads to?
The protein prevents gene mutation
Unreliable results
approximately 53 times before it denatures
Good results
The protein consists of 53 amino acids
Reproducable results
Reliable results
Question 2: The proteins migrate through
two different layers in the gel: the stacking
Question 28: How many sets of primers are
gel and the separating gel. What is the
needed for DNA profiling?
purpose of the stacking gel?
13
1
The pH of the stacking gel sets the pace preparation after we have extracted the DNA
of migration, ensuring that all proteins from the bone?
start in the separating gel at the same Perform end-repair
time Perform A-overhang
The stacking gel has the same purpose as Ligate the adapters
the separating gel Perform fragmentation
The pH of the stacking gel folds the proteins
into a specific structure that allows them to Question 6: Why do we skip the
move through the gel fragmentation part when we are sequencing
The stacking gel holds the separating gel in ancient DNA like this sample?
its position Because the DNA is already partially
degraded
Because the DNA contains G - A base
Next Generation Sequencing substitution
Because we need to process the DNA
Question 1: How many clusters do you think immediately
we have in one flow cell? Because the fragmentation costs a lot of
200 million money
20 million
2 million Question 7: What is the purpose of the end-
200,000 repair procedure?
To create blunt-ended strands
Question 2: There are many advantages of To create a double strand
using the Next Generation Sequencing (NGS) To create a hairpin loop
technique as compared to the Sanger To create sticky end strands
sequencing. Which one of these is an
advantage of NGS? Question 8: What is the next step after end-
We can sequence many DNA molecules repair?
in parallel Adding adenine to the 3' end of the
It takes a longer time to sequence DNA with strand
other techniques Adding aspartic acid to the 3' end of the
We can use fluorescence-labeled bases strand
We can sequence only very long DNA strands Adding RNA to the 3’ end of the strand
Adding arginine to the 3' end of the strand
Question 3: What are the possible
applications of NGS? Question 9: Why do we need an adenine
All of these options overhang?
Detecting genetic aberration To ensure that the adapters bind
Perform gene expression profiling specifically
Perform SNP profiling To precipitate the DNA
To create a longer strand
Question 4: What is the first step that you We do not need it, the Taq adds it
need to do to prepare the bone sample for automatically
DNA sequencing?
Extract the DNA Question 10: What is the purpose of the
Perform A-overhang adapter?
Ligate the adapters For the PCR primers to bind to it
Perform fragmentation To synthesize more DNA
To ligate one DNA strand to the other
Question 5: When sequencing ancient DNA, To make the DNA strands a bit longer
what is the next step in the sample
Question 11: We only run PCR amplification
for 10-12 cycles which is much lower than Question 17: After bridge PCR amplification,
the usual 30 cycles. What is the reason for half of the DNA strands are washed away.
this? Why?
Minimizing error introduced in To sequence clusters of identical
replication due to lower sample quality (clonal) DNA
We have plenty of DNA to begin with Because there's not enough sequencing
The ancient DNA cannot withstand repeated primer
high temperatures To only sequence the tightly bound DNA
The PCR reagents are too expensive strand
Because it is too crowded to sequence 4,000
Question 12: Now that we have performed strands at the same time
the PCR amplification and accumulated
enough DNA, what is the next step? Question 18: Which enzyme is used in the
Generating clusters sequencing process?
Data analysis T4 DNA polymerase
Adapter ligation T4 Deoxynucleotide kinase
Sequencing T4 Exonuclease
T4 DNA ligase
Question 13: What is currently happening?
The DNA molecules are binding to the Question 19: In the next generation
short DNA molecules on the flow cell sequencing, each of the bases is tagged so
The DNA molecules are being amplified that we can specifically identify them. What
The DNA molecules are being ligated to the is this tag?
adapter Fluorophore
The adapter is being replicated Phosphate
Kinase
Question 14: How could the DNA molecules Biotin
bind to the adapter on the flow cell?
Because the sequences are Question 20: How many pictures are taken
complementary for every single base addition?
Because one strand is positively charged and Four
the other is negatively charged Three
It occurs by chance Two
Due to their proximity One

Question 15: What is the name of the Question 21: When we are sequencing from
process that is currently shown in the only one direction, the process is also called?
animation, where the DNA molecules bend Single-end sequencing
and bind each end to an adapter on the flow Single-molecule sequencing
cell? Uni-directional sequencing
Bridge PCR Paired-end sequencing
Pyro PCR
Microdroplet PCR Question 22: The sequencing outcome is
Emulsion PCR stored, including the sequence and quality.
What is this file called?
Question 16: How many DNA molecules are FASTQ
produced in each cluster? WIG
4,000 SAM
40,000 BAM
400
40
Question 23: In a FASTQ file, what is the Hairy ears
Phred quality score? Wet earwax
The probability of an incorrect base
calling for each base Question 29: The ancient Greenlandic man
The accuracy of sequencing of a known tag carries two C alleles for Rs1129038. What is
The number of reads for each base the most likely color of his eyes?
The percentage of bases that could not be Brown
determined Orange
Green
Question 24: The Phred scale describes the Blue
probability of the error when calling a base.
What is the probability of an incorrect base Question 30: Which trait is an individual with
call for a quality score of 40? a G in SNP Rs6152 likely to have?
1 in 10,000 Developing baldness
1 in 1,000 Having red hair
1 in 100 Having short hair
1 in10 Having blonde hair

Question 25: In the secondary data analysis, Question 31: With the allele of C/C on
we assemble all the reads and try to Rs3827760, what shape were the ancient
interpret the data. What should we do first Greenlandic man's teeth most likely?
before starting the secondary analysis? Shovel-shaped
Trim out the adapters Diamond-shaped
k-mer correction Peg-shaped
Perform SNP analysis Sub-circular shaped
Assemble reference genome
Question 32: What skin color did the ancient
Question 26: Since we are working with Greenlandic man likely have due to G instead
ancient DNA, we need to be able to identify of A in SNP Rs1426654?
whether it has been contaminated with Non-light skin
modern human DNA. Which characteristic Yellow skin
below is NOT found in ancient DNA? Black skin
It is structured into very long strands Light skin
Often has a G > A conversion in the 3' end
It often is degraded into fragments around
50 bp long
Often has a C > T conversion in the 5' end

Question 27: There are two ways to do an

assembly depending if you know the
reference sequence or not. What are they
called?
Alignment and de novo assembly
Local and global
Sorted and indexed
Small and large

Question 28: This man carries two T alleles

for Rs17822931, what is the most likely
phenotype for this SNP?
Dry earwax
Non-hairy ears