Tom is a molecular biology graduate student who needs to isolate a gene from the pathogenic bacteria Salmonella typhi, which he is studying. He wiselydecides to use PCR to amplify the gene before trying to purify it. The gene has the general structure shown below:
~1000 Base Pairs ! ! 5â-ATGGCTTACGTG-----------CCATAGGGCTAA-3â ! ! 3â-TACCGAATGCAC-----------GGTATCCCGATT-5â
The gene is about 1000 nucleotide base pairs long, but only the sequences at the ends of the double strand are shown. Use the information from the video, what you learned about base pairing in class, and the fact that PCR always proceeds along the parent DNA strand the 3â to 5â direction. Design two, 6-nucleotide long, PCR primers for Tom. When you have these primers designed, proceed to the âExercises and videosâ link. You will be prompted for important information in drop-down menus. Answer each question and click continue to see a first-person performance of a PCR reaction.
Question #1 (These will be multiple choice and are automatically graded) a) What different components will do you want to add to your PCR?
b) Which primers will you use?
c) How many PCR cycles should you set the thermocycler for to obtain 128 TOTAL strands of DNA at the end of the reaction (this includes the template strands that you started with)?
d) To analyze the PCR you need to make a DNA gel. What do you want to add to make the gel?
Tom is a molecular biology graduate student who needs to isolate a gene from the pathogenic bacteria Salmonella typhi, which he is studying. He wiselydecides to use PCR to amplify the gene before trying to purify it. The gene has the general structure shown below:
~1000 Base Pairs ! ! 5â-ATGGCTTACGTG-----------CCATAGGGCTAA-3â ! ! 3â-TACCGAATGCAC-----------GGTATCCCGATT-5â
The gene is about 1000 nucleotide base pairs long, but only the sequences at the ends of the double strand are shown. Use the information from the video, what you learned about base pairing in class, and the fact that PCR always proceeds along the parent DNA strand the 3â to 5â direction. Design two, 6-nucleotide long, PCR primers for Tom. When you have these primers designed, proceed to the âExercises and videosâ link. You will be prompted for important information in drop-down menus. Answer each question and click continue to see a first-person performance of a PCR reaction.
Question #1 (These will be multiple choice and are automatically graded) a) What different components will do you want to add to your PCR?
b) Which primers will you use?
c) How many PCR cycles should you set the thermocycler for to obtain 128 TOTAL strands of DNA at the end of the reaction (this includes the template strands that you started with)?
d) To analyze the PCR you need to make a DNA gel. What do you want to add to make the gel?
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Related textbook solutions
Related questions
QUESTION 1
A mutation caused by exposure to gamma rays is called a spontaneous mutation
a. | True | |
b. | False | |
c. | Sometimes, depending on the type of base change | |
d. | Gamma rays do not cause mutations |
QUESTION 2
A recessive mutation affecting an essential biochemical pathway can be detected________
a. | when the organism is heterozygous for that mutation. | |
b. | when the organism is homozygous for that mutation. | |
c. | in either homozygous or heterozygous conditions. | |
d. | only by sequencing (recessive mutations never show a phenotype). |
QUESTION 3
During DNA replication, the newly synthesized chain grows by adding
a. | nitrogenous bases | |
b. | the sugar-phosphate backbone | |
c. | nucleosides | |
d. | dNTPs |
QUESTION 4
During replication, the DNA strand 5â- AAGTCTAGCCTAG -3â will serve as a template for the polymerization of:
a. | 5â- CTAGGCTAGACTT -3â | |
b. | 5â - TTCAGATCGGATC -3â | |
c. | 5â - GATCCGATCTGAA -3â | |
d. | 3â - AAGTCTAGCCTAG -5â |
QUESTIOn 5
Given the following DNA sequences, select which statement(s) is(are) correct.
Sequence 1:
5â-TGGACGCTAA-3â
3â-ACCTGCGATT-5â
Sequence 2:
5â-AATCGCAGGT-3â
3â-TTAGCGTCCA-5â
Sequence 3:
5â-ACCTGCGATT-3â
3â-TGGACGCTAA-5â
a. | Sequences 1 and 2 are the same | |
b. | Sequences 1 and 3 are the same | |
c. | Sequences 2 and 3 are the same | |
d. | Sequences 1, 2 and 3 are all different |
QUESTION 6
Repetitive sequences in the genome are hotspots for:
a. | Deamination | |
b. | Depurination | |
c. | Thymine dimer formation | |
d. | Replication errors |
QUESTION 7
Select which statement(s) about the Ames test is(are) correct
a. | it has been designed to understand mutation repair systems in Salmonella typhimurium | |
b. | it uses mammalian liver extract | |
c. | it allows to study whether chemical compounds or their enzymatic breakdown products are mutagenic | |
d. | it is based on whether a chemical compound causes reversion mutations from his+ to his- | |
e. | two of the above are correct | |
f. | three of the above are correct |
QUESTION 8
Select which statement(s) is(are) correct.
a. | All DNA strands have a direction, and it is specified by the carbons in the sugar backbone. | |
b. | All DNA strands have a direction, and it is specified by hydrogen bonds between nucleotides. | |
c. | In order to form proper base pairs in a double stranded DNA molecule, the two strands must run in opposite directions. | |
d. | A and C are correct. | |
e. | B and C are correct. |
QUESTION 9
Studies of gene mutation frequencies have shown that:
a. | mutations are rare, and genomes are generally stable. | |
b. | mutation frequencies differ among organisms and also between genes, suggesting certain genes are more susceptible to mutation. | |
c. | mutation frequencies are consistent between organisms, and each region of DNA is equally susceptible to random mutations. | |
d. | Both A and B are correct. | |
e. | Both A and C are correct. |
QUESTION 10
The compound 5-bromodeoxyuridine (BrdU) is a derivative of uracil, and if BrdU becomes incorporated during DNA replication, it pairs with adenine. This compound is best classified as which type of mutagen?
a. | base analog | |
b. | base inducer | |
c. | intercalating agent | |
d. | oxidative agent | |
e. | alkylating agent |
QUESTION 11
The rate of mutation of the fruit fly is higher than the rate of mutation of Algae
True
False
QUESTION 12
Thymine dimers are most commonly caused by which of the following?
a. | X-rays | |
b. | Alkylating agents | |
c. | U.V. irradiation | |
d. | DNA intercalating agents |
QUESTION 13
What chemical group is found in the 3â end of a DNA strand?
a. | an alcohol | |
b. | a hydroxyl | |
c. | a methyl | |
d. | a phosphate |
QUESTION 14
What chemical group is found in the 5â end of a DNA strand?
a. | an alcohol | |
b. | a hydroxyl | |
c. | a methyl | |
d. | a phosphate |
QUESTION 15
Which is the correct order of molecules binding to DNA during DNA replication?
a. | Helicase, SSB, primase, DNA pol III, DNA pol I, ligase | |
b. | SSB, DNA pol I, ligase, helicase, DNA pol I, primase | |
c. | primase, helicase, DNA pol III, ligase, DNA pol I, SSB | |
d. | SSB, helicase, primase, DNA pol III, DNA pol I, ligase |
QUESTION 16
Which statement(s) is(are) correct about strand slippage?
a. | It can cause disorders such as Huntingon disease. | |
b. | It is a process that causes mutations altering the number of DNA repeats. | |
c. | It is a process that incorporates nucleotide base analogs and trinucleotide repeats. | |
d. | a and b are correct. | |
e. | b and c are correct. | |
f. | a, b and c are correct. |
help needed asap.