Download DNA Questions #4 Questions on the PCR Process:

DNA Questions #4
Fo Sci
Name __________Key_____________________________
Use PPT slides 19-30 to answer the following questions.
Questions on the PCR Process:
Once the DNA is extracted, it is placed in a micro centrifuge tube that contains nucleotides,DNA polymerase and
primers for the ends of the target sequences. The tubes are placed in a thermocycler to warm and cool the DNA in
cycles. Warming causes the strands to separate so that the primers can bind to the DNA and the DNA polymerase can
add nucleotides to the single strands. Cooling stabilizes the newly formed strands.
44) A primer is shown to the right. It is best described as
a.
a short sequence of nucleotides that is complimentary to a sequence of nucleotides in the middle of an STR
target sequence.
b. a sequence of nucleotides that can bind to the end of an STR to help begin amplification or replication of the
DNA.
c. a sequence of nucleotides that binds to the entire STR.
45) In order for a primer to anneal or bind to a segment of DNA, the DNA must be _____________ so that it will
separate into two strands
a.
replicated
b. primed
c. heated
46) The following is a typical target sequence of DNA at an STR site. You will need to identify the repeated
sequence in the upper strand. It is composed of 4 nucleotides. This repeat does not start at the far left of the
upper strand. The primer binding region at the upper left is where the primer will bind. The repeat is to the
right of that primer. Note that the underlined primers are different for the upper and lower strand.
-A T C G T T C A T T C A T T C A T T C A T T C A T G G C A T-
upper strand
-T A G C A A G T A A G T A A G T A A G T A A G T A C C G T A-
lower strand
a) What is the sequence of the 4 nucleotide repeat in the upper strand? __TTCA____________________
b)
How many repeats are there in the upper strand? __5__________________
c)
What is the sequence of the forward primer (binds to the upper, left sequence) ? ___TAGC___________
d) What is the sequence of the reverse primer (binds to the lower, right sequence)? ____TGGCAT________
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47) What is the name of the tool shown below that is used to amplify
numerous samples at the same time?
____Thermocycler___________________
What does this tool do? __Heats , cools and holds the _______
microcentrifuge tubes with DNA during the PCR process.______
48) Why is PCR used during the process of DNA profiling?
_____It amplifies or makes billions of copies of the DNA so it can be visualized. You only need small samples of the
original DNA for the PCR process. That allows scientists to determine a DNA profile from materials as scant as a from
dental molds, cigarette butts, eating utensils, chewing gum, postage stamps, ski masks, licked envelopes, toothbrushes,
razor shavings, band-aids and fingerprints.______________________________________________________________
_____________________________________________________________________________________________
Questions on the Gel Electrophoresis Process:
49) Which of the following processes is responsible for visualizing the DNA?
a. extraction
b. amplification
c. gel electrophoresis
d. centrifugation
50) Why is it necessary to run a gel electrophoresis after the PCR?
___You cannot visualize of see the DNA bands on the gel unless they have been amplified to billions of copies.
PCR amplifies the target sequences so you end up with billions of copies._______________________________
___________________________________________________________________________________________
51) In order for a gel tray to separate different sizes of DNA fragments, which of the following must be a chemical
characteristic of DNA?
a.
it is symmetrical
b. the nucleotides must be complimentary
c. the molecule must be charged
52) When analyzing nDNA, ____________________ is always done before _____________________.
NOTE: There are two correct answers!
a. Gel electrophoresis ; PCR
b. PCR ; Gel electrophoresis
c. amplification : visualization
d. visualization ; amplification
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Use PPT slides 30-36 to answer the following questions.
Use the following visual to help you answer the questions below:
WELL
+
_
53) Based on what you know about the charge of a DNA molecule, what direction will the DNA that is loaded into
the wells on the left travel?
a. To the left, toward the positive charge because DNA has a negative charge
b. To the right, toward the negative charge because DNA has a positive charge
54) In a gel electrophoresis tray, the shorter target sequences travel faster and further than the longer sequences.
a. true
b. false
55) Which of the following segments of DNA would travel faster away from the negative charge on a gel plate?
a. an STR with four repeats
b. an STR with 10 repeats
56) Which of the following segments of DNA would travel faster to the + charge on the gel plate?
a. an STR with four repeats
b. an STR with 10 repeats
57) A person who is heterozygous for 3 and 7 repeats will show ____2_______ band(s) on the gel.
58) A person who is homozygous for a 3 repeat will show ____1________ band(s) on the gel.
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DNA Questions #5
Fo Sci
Name ____________Key___________________________
Use PPT slides 30-38 to answer the following questions.
Another way of saying the same thing, “The purpose of PCR is to make copies of the sample and the purpose of gel
electrophoresis is to visualize or see the sample.
59) A DNA ladder is a sample that is tested in a well along with the regular samples in a gel electrophoresis. The
ladder is a sample composed of known repeats with different base pair (bp) sizes. They come out as a
continuous string of bands along one side or down the center of the gel. The scientist KNOWS the size of the
molecules in each of the bands.
For example: The ladder run below shows the location on a gel where bands composed of 2,000, 800, 400 and 200 base
pairs of nucleotides would show up. A sample is run at the same time in a well next to the well the ladder is in. If the
band for that sample comes out in the same location as the 800bp band on the ladder, we know that the sample has
target sequences that are 800 base pairs long.
60) Given the ladder below, draw a band for a sample in well #2that would contain target sequences that are 400
base pairs long:
WELL #2
a)
b)
c)
d)
Each band contains thousands
of target sequences that are all
the same size. If PCR had not
been done before
electrophoresis, you would not
be able to see the bands at all!
61) A ladder is used to
a) Determine the number of target sequences in the band.
b) Determine the length of target sequences ( in base pairs-bp) in the band.
c) Is not helpful when analyzing the DNA.
d) Contains random DNA sequences that the scientist does not know the length of.
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62) Given the following gel results:
1
2
3
300 bp
275 bp
250 bp
225 bp
200 bp
175 bp
150 bp
125 bp
a)
The sample in lane #1 is the ____ladder______________( ladder, STR target sequence).
b)
The sample in lane #2 is from a person who is ____homozygous___(homozygous, heterozygous) for the STR.
c) The band in lane #2 is approximately __265________ base pairs (bp) long.
d) The largest target sequences in lane #3 are approximately ____290__________ bp long.
e) Each band on the electrophoresis gel is composed of ___1,000’s____(1, 10, 100’s, 1,000’s) of target sequences.
f)
Given the following gel results for the FGA STR, which lane contains a DNA sample that is a match to the sample
in lane #1? __sample in lane #2___
Lane 1
Lane 2
Lane 3
g) If the sample In lane #1 is from
the suspect and the sample in lane 3
is evidence from the crime scene,
can you connect the suspect to the
scene?___NO!_____________
h) Is the person who contributed the sample in lane 3 homozygous or heterozygous for the FGA STR?
___hetero_____
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Fo Sci
DNA Questions #6
Name _____________Key________________________
Use all remaining PPT slides to answer the following questions.
63) Label the lane that contains the ladder
in the gel to the right
64) Simultaneous analysis of different STR’s at the same time is called __multiplexing_________.
65) What is the difference between gel and capillary electrophoresis? Write the words “Gel electrophoresis” or
“Capillary electrophoresis” or “Both” next to each of the statements below:
a. Uses a polyacrylamide or agar gel in a horizontal bed or plate. __Gel________________________________
b. Uses a gel in a narrow tube called a capillary tube. ____Capillary___________________________________
c. Results cannot be seen but must be interpreted by a computer. ___Capillary__________________________
66) Which of the following are true about the TPOX STR? (Choose all that apply)
a. Every person has two alleles for TPOX
b. TPOX alleles are sequences that code for important proteins.
c. The alleles in the TPOX region can be visualized using capillary electrophoresis or gel
electrophoresis.
d. The TPOX is found in mtDNA.
67) The D21 STR tends to have alleles that range from 180-220 base pairs (bp) in length. Given the following
multiplex electropherogram result, is the person homozygous or heterozygous for the D21 STR? _two peaks,
heterozygous_____
68) What are the three possible outcomes of a DNA Profile? (Check your PPT)
a. ___match______
b. ___exclusion______
c. ____inconclusive______
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69) The amelogenin gene codes for a protein found in tooth enamel. It is found on the X AND Y sex chromosomes.
The AMELX gene on the X chromosome is composed of only 109 bp. The AMELY gene on the Y chromosome is
composed of 112 bp. These genes are used in multiplexing of STR’s as a check to make sure the sex of the
person and sample are the same. If the sample is from a female, it will show only one peak for AMELX at 109 bp.
If the sample is from a male, there will be two peaks. One will be for AMELX at 109 bp and one for AMELY at
112 bp. The two peaks will be very close to each other at the beginning of the electropherogram, before any of
the other STR’s. Using the same bp scale as in the report above, determine the sex of the person who submitted
the samples above __male______ and the sample below.____female__________ (they are not the same).
70) Name 4 different applications of DNA Profiling:
b. ____Paternity testing________________
c. _____Personal identification_____________
c. ____Forensic matching_______________
d. _____Historical investigations____________
Note: DNA profiling is not commonly used for identification of people in the general population (like yourself) because
even though it only uses part of your DNA, the original sample that is taken could be used to determine your entire
genotype (all the DNA sequences) and could be used by insurance companies to deny you coverage if you have a gene
that codes for a disease.
71) What is the data base that contains DNA Profiles from federal convicts and convicted felons?
a. AFIS
b. CODIS
Probabilities:
72) The ____smaller______(smaller, larger) the frequency (probability) of having an STR allele, the
__greater___________ (greater, less) the value in DNA fingerprinting. (There are two different answers heresmaller, greater and larger, less.)
Explain why: _____Like identifying people in a room, it is better to use a characteristic like, “wears pink colored
glasses” (not as common or frequent) than a characteristic like brown hair (very common).___STR repeats that
are not very common in the population will be much more helpful in identifying a person than an STR repeat
that is very common. _______________________________________________________________________
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