Biochemistry CH6: DNA & Biotechnology
Describe what happens during each step of PCR and why the temperature is set to what it is during each step: (1) Denaturation (96° C) (2) Annealing (55° C) (3) Extension (72° C)
(1) Denaturation - The double stranded DNA that you are interested in studying is denatured as the temperature is increased to 96° C. (2) Annealing - As the temperature is decreased to 55° C, the primer anneals to the end of the region that you want to copy on each strand of DNA. (3) Extension - DNA Polymerase (which is most active at a temperature of 72° C) begins extending the DNA from the primer.
The backbone structure of DNA from top to bottom reads as follows: Phosphate-C5-Sugar-C3-Phosphate-C5-Sugar-C3... What is the direction in which this DNA backbone is oriented? Synthesized? (A) 5' to 3' (B) 5' to 5' (C) 3' to 3' (D) 3' to 5'
(A) 5' to 3' for both The DNA backbone is oriented in 5' to 3' direction, having the 5' Carbon before the 3' Carbon. DNA is ALWAYS synthesized in the 5' to 3' direction!
Telomeres are extremely repetitive. They consist of which sequence repeated over and over again? (A) 5'GGTTAG3' (B) 5'GTTTAA3' (C) 5'GGGTTG3' (D) 5'GCTAAG3'
(A) 5'GGTTAG3' Mnemonic: "Go Go Telomeres! Telomeres Are Great!"
What are the four nitrogenous bases that make up the "rungs" of a DNA molecule, connecting the two strands? (A) Adenine, inosine, uracil, and guanine (B) Adenine, thymine, inosine, and guanine (C) Adenine, thymine, cytosine, and uracil (D) Adenine, thymine, cytosine, and guanine
(D) Adenine, thymine, cytosine, and guanine Adenine, thymine, cytosine, and guanine are the four bases that make up DNA.
CRB When DNA Repair processes fail, cancer is likely to follow. Which of the following would likely cause an increased risk of cancer? I. Breaking the DNA backbone II. Altering bases and base pairs III. Incorporating incorrect bases during replication. (A) II only (B) I and III only (C) II and III only (D) I, II and III
(D) I, II and III Each of the following could increase the risk of cancer: I. Breaking the DNA backbone II. Altering bases and base pairs III. Incorporating incorrect bases during replication.
Which of the following statements about Base Excision Repair are true? I. Base Excision Repair can detect non-helix distorting mutations II. Base Excision repair will remove the affected base using a Glycosylase Enzyme. III. An AP Endonuclease will then remove the damaged DNA sequence, so DNA polymerase and ligase can finish the repairs. (A) III only (B) I and II only (C) I and III only (D) I, II and III
(D) I, II and III Each of the following statements about Base Excision Repair are true: I. Base Excision Repair can detect non-helix distorting mutations II. Base Excision repair will remove the affected base using a Glycosylase Enzyme. III. An AP Endonuclease will then remove the damaged DNA sequence, so DNA polymerase and ligase can finish the repairs.
CRB Which of the following statements relating to the Nitrogenous Bases are true? I. All five of the nitrogenous bases are aromatic. II. All five of the nitrogenous bases are planar and cyclic. III. All five of the nitrogenous bases form heterocyclic compounds. (A) I only (B) II only (C) II and III only (D) I, II and III
(D) I, II and III Each of the following statements are true: I. All five of the nitrogenous bases are aromatic. II. All five of the nitrogenous bases are planar and cyclic. III. All five of the nitrogenous bases form heterocyclic compounds
Which of the following are functions of telomeres? I. Protect the chromosome from deterioration. II. Prevent the chromosomes from sticking together. III. Prevent the loss of genetic information with each round of replication. (A) I Only (B) I and II Only (C) II and III Only (D) I, II, and III
(D) I, II, and III Telomeres are the cap ends of chromosomes and they serve as a protection for the chromosomes from deterioration. Telomeres also prevent the chromosomes from sticking to each other. They also help prevent the loss of genetic information in each round of replication, because telomeric sequences indicate to the enzyme that it has reached the end of the chromosome.
Which enzyme(s) is/are required in proofreading, mismatch repair, and nucleotide excision repair? I. Endonuclease II. DNA Polymerase III. DNA Ligase (A) I Only (B) II Only (C) I and III Only (D) II and III Only
(D) II and III Only Proofreading, mismatch repair, and nucleotide excision repair all require the support of DNA polymerase to fill in the gap and DNA ligase to seal the strand.
Which of the following statements about Proto-oncogenes and Antioncogenes is NOT true? (A) Antioncogenes are often called Tumor Suppressor Genes (B) Proto-oncogenes typically code for cell-cycle related proteins. (C) Even one functional copy of an antioncogene is typically enough to inhibit tumor formation. (D) Oncogenes could be described as speeding up the cell cycle, and antioncogenes are like cutting the brakes.
(D) Oncogenes could be described as speeding up the cell cycle, and antioncogenes are like cutting the brakes. Having non-functional (mutated) antioncogenes are like cutting the brakes.
Fill in the blanks: __________________ are genes that, if one copy is mutated, then they can cause cancer. ____________ are genes that would need both copies to be mutated to promote cancer. (A) Oncogenes, Proto-oncogenes (B) Oncogenes, Antioncogenes (C) Antioncogenes, Proto-oncogenes (D) Proto-oncogenes, antioncogenes.
(D) Proto-oncogenes, antioncogenes. Proto-oncogenes are genes that, if one copy is mutated, then they can cause cancer. Antioncogenes are genes that would need both copies to be mutated to promote cancer.
True or False? Telomeres are usually found in both eukaryotes and prokaryotes. False. Telomeres are found in the chromosomes of eukaryotic cells and NOT prokaryotic cells because prokaryotic cells have circular chromosomes that do not have ends. Out of the three proposed ways in which DNA can be replicated, which theory is experimentally proven? (A) Conservative (B) Dispersive (C) Liberal (D) Semi-conservative
(D) Semi-conservative Semi-conservative DNA replication is the proven method of DNA replication. The Meselson-Stahl experiment proved this.
Which repair mechanism is responsible for fixing Pyramidine Dimers? (A) The DNA Polymerase III Proofreading Mechanism (B) The Base Excision Repair Mechanism (C) The Mismatch Repair Mechanism (D) The Nucleotide Excision Repair Mechanism
(D) The Nucleotide Excision Repair Mechanism Nucleotide excision repair is used to remove and repair pyrimidine dimers.
What is the role of histone proteins? (A) To mechanically support the nucleus and prevent the nuclear membrane from folding in on itself. (B) To maintain the integrity of the chromosomes by protecting them from free radical damage (C) To store nucleotides when synthesis and transcription are not actively occuring. (D) To tightly bind and condense DNA during interphase into chromosomes.
(D) To tightly bind and condense DNA during interphase into chromosomes. Histones tightly bind and condense DNA during interphase into chromosomes, turning long stretches of DNA into packages small enough to be held within the nucleus.
Adenine will base pair with _________. Cytosine will base pair with __________. (A) adenine, cytosine (B) guanine, thymine (C) thymine, adenine (D) thymine, guanine
(D) thymine, guanine In DNA, the base, adenine, is always paired with the base thymine (A-T), and cytosine always pairs with guanine (C-G).
What is a pyrimidine dimer?
A pyrimidine dimer is a type of DNA damage in which two pyrimidine nucleotides (typically thymine) are stuck together. The structural damage of pyrimidine dimers includes the protrusion of phosphate backbone and the breaking of hydrogen bonds between adjacent nucleotide base pairs.
Which of the following may happen to a cell that has accumulated a lot of DNA damage and/or mutations? I. The cell enters a dormant state and cell does not divide anymore. II. The cell dies. III. The cell becomes a cancer cell due to unregulated cell division. (A) I Only (B) I and III Only (C) II and III Only (D) I, II, and III
CRB Describe how UV Light and multiple Thymines on the same strand could require the Nucleotide Excision Repair mechanism to function. UV light can excite the electrons of Thymines and cause neighboring Thymines to bond, forming a Thymine Dimer, distorting the double-helix and proper functions. The Nucleotide Excision Repair mechanism will recognize this error and replace the affected DNA section. Which of the following may happen to a cell that has accumulated a lot of DNA damage and/or mutations? I. The cell enters a dormant state and cell does not divide anymore. II. The cell dies. III. The cell becomes a cancer cell due to unregulated cell division. (A) I Only (B) I and III Only (C) II and III Only (D) I, II, and III (D) I, II, and III A cell that has accumulated a lot of DNA damage and/or mutations may engage in any of the following: I. The cell enters a dormant state and cell does not divide anymore. II. The cell dies. III. The cell becomes a cancer cell due to unregulated cell division.
Which of the five nitrogenous bases are pyrimidines?
Cytosine, uracil (found in RNA only), and thymine (found in DNA only) are all part of the pyrimidine family. All three have one ring.
How are the role of Helicase and Replication Forks linked?
DNA Helicase unwinds the parent strands of DNA. Replication forks are the boundary where new DNA is being transcribed, near the DNA Helicase's activity.
True or false? DNA Ligase, which is also involved in linking Okazaki Fragments, can also proofread the DNA.
DNA Ligase, which is also involved in linking Okazaki Fragments, cannot proofread the DNA.
Why is DNA Polymerase from Thermus aquaticus (Taq, a bacteria that lives in the hot springs of Yellowstone National Park) used instead of DNA Polymerase from a human or bacteria?
DNA polymerase from Thermus aquaticus (Taq, a bacteria that lives in the hot springs of Yellowstone National Park) is very heat resistant, meaning that it will not denature at the high temperature required to denature the DNA strands (96° C). If human or bacteria DNA Polymerase was used, the enzyme would denature and not work.
What is the difference between endogenous agents vs exogenous agents when talking about DNA damage?
Endogenous agents are internal factors, such as reactive oxygen species found within our own cells, that can cause DNA damage. Exogenous agents are external factors, such as UV rays, gamma rays and x-rays, that can cause DNA damage.
What is the difference between exonuclease activity and endonuclease activity?
Enzymes engage in exonuclease activity when they remove an incorrect nucleotide from the end of a DNA strand. Enzymes engage in endonuclease activity when they remove an incorrect nucleotide from the middle of a DNA strand.
True or false? Because DNA is always synthesized in the 5' to 3' direction, new phophodiester bonds are formed at the growing strand's 5' Hydroxyl Group.
False. Because DNA is always synthesized in the 5' to 3' direction, new Phosphodiester bonds are formed at the growing strand's 3' Hydroxyl Group.
True or False? It is easier to denature DNA with a lot of Cytosine-Guanine bonds at lower temperatures because it has more hydrogen bonds than the Adenine-Thymine bonds.
False. It is harder to denature DNA with a lot of Cytosine-Guanine pairs at lower temperatures because it has more hydrogen bonds than the Adenine-Thymine pairs. The C-G pairing has 3 hydrogen bonds, making it relatively more stable than the A-T pairing with 2 hydrogen bonds.
True or False? Telomeres are usually found in both eukaryotes and prokaryotes.
False. Telomeres are found in the chromosomes of eukaryotic cells and NOT prokaryotic cells because prokaryotic cells have circular chromosomes that do not have ends.
Imagine that Martians have nucleotides where both the 3' and 5' Carbons had Hydroxyl groups attached and formed ether bonds to join nucleic acids. Would their DNA be considered Antiparallel?
If both the 3' and 5' had Hydroxyl groups, it would be impossible to determine which end were which. This means these DNA strands have no polarity, so they could not be anti-parallel!
Compare Nucleotides and Nucleosides, focused on the main components Nucleotides are made of.
Nucleosides contain the five-carbon sugar and nitrogenous base, but do not have any phosphate groups. A Nucleoside becomes a Nucleotide when a Phosphate Group is added to it.
Which DNA will travel the farthest during gel electrophoresis? A DNA with 6,000 base pairs or DNA with 3,500 base pairs?
The DNA with 3,500 base pairs will travel farther during gel electrophoresis because the gel acts like a sieve, allowing small particles to travel through more easily while retaining large particles; consequently, shorter DNA will travel farther through the gel.
Working on a research project, you run a gel electrophoresis on some DNA samples. Subsequently, you find out from your principal investigator that your DNA samples have been damaged during the gel electrophoresis. You find out that the buffer solution in which you bathed the DNA was acidic. Why did this damage your DNA and ruin your gel electrophoresis?
The acidic solution lilkely affected the charge on the DNA due to the protonation of phosphate groups. This affected the rate at which the DNA migrated towards the positive electrode.
What does it mean to say that DNA has an "antiparallel structure"?
The antiparallel structure of DNA describes two parallel DNA strands that are oriented in opposite directions (one in the 5' to 3' direction and the other in the 3' to 5' direction).
What are the relative benefits of agarose (polyacrylamide gel) compared to sodium dodecyl sulfate (SDS)-polyacrylamide gel?
The benefits of agarose gel (polyacrylamide gel) are that it allows a complete protein to be recovered after an analysis since SDS is a denaturant and can damage DNA or denature proteins, and secondly the agarose gel (polyacrylamide gel) determines the globular size of proteins.
What does the enzyme telomerase do?
The enzyme telomerase lengthens the telomeres and brings them back to their original length.
What is the purpose of gel electrophoresis?
The purpose of Gel Electrophoresis is to figure out the size and charge of macromolecules such as DNA, RNA and proteins.
What is the structural difference in ribose vs deoxyribose?
The structural difference between ribose and deoxyribose is at the second carbon (C-2). The ribose has an -OH group at C-2, while deoxyribose has a -H at C-2.
What is conservative DNA replication?
The theory of conservative DNA replication describes when the two original template DNA strands stay together in a double helix and produce a copy composed of two new strands.
What is semi-conservative DNA replication?
The theory of semi-conservative DNA replication describes when each daughter DNA double helix has one old strand and one newly synthesized strand.
How many hydrogen bonds exist between thymine and adenine? Cytosine and guanine?
There are 2 hydrogen bonds between thymine and adenine. There are 3 hydrogen bonds between cytosine and guanine.
Compare senescence versus apoptosis.
To say a cell is senescent means that the cell no longer divides. Apoptosis is programmed cell death in which a cell digests/destroys itself.
How does Topoisomerase make Helicase's job easier?
Topoisomerase is responsible for removing DNA supercoils, unwinding the tightly wound DNA helix, making it easier for the enzyme helicase to cut through the middle of DNA.
True or false? Base Excision repair would notice if a Cytosine is Deaminated (forming a Uracil) and trigger that repair.
True. Base Excision repair would notice if a Cytosine is Deaminated (forming a Uracil) and trigger that repair.
True or False? Proofreading takes place during replication.
True. Proofreading (the correction of misplaced nucleotides) takes place during replication.
True or false? Sometimes the Nucleotide Excision Repair mechanism needs to function even when the DNA had been properly transcribed.
True. Sometimes the Nucleotide Excision Repair mechanism needs to function even when the DNA had been properly transcribed.
True or False? If the hydrogen bonds were mutated within the Nitrogenous bases, the double helix would no longer form.
True. The DNA would not be able to form the double helix structure because the nitrogenous base pairs are held together by hydrogen bonds.
What would happen to a cell that loses all of its telomeres?
When a cell loses all of its telomeres, the cell does not divide anymore and will die.
What would you expect to see when comparing the telomere length of an adult's chromosomes vs a child's?
When comparing the chromosomes between an adult and a child, you would expect to find that a child's chromosome has a longer telomere than in the adult's chromosome. This occurs because telomeres shorten over time (with each replication).
Which of the following is the proper name for the bond between phosphate groups (e.g. between the gamma and beta phosphate groups in ATP)? (A) Anhydride (B) Hydride (C) Ester (D) Phosphodiester
(A) Anhydride Between multiple covalently-bound phosphate groups are an anhydride linkage.
Which of the following is best described as the opposite of denaturing DNA, where the complementary strands become paired? (A) Annealing (B) Binding (C) Conjoining (D) Combining
(A) Annealing Annealing is the opposite of denaturing DNA, and when the complementary strands become paired.
Where do the nitrogenous bases bind to the backbone of DNA? (A) C-1 of deoxyribose (B) C-2 of deoxyribose (C) C-5 of deoxyribose (D) O of Phosphate
(A) C-1 of deoxyribose The nitrogenous bases bind to the first carbon (C-1) on the sugar group of the backbone.
The structural backbone of DNA has been compromised by a rare pathogen. This pathogen must have disrupted what type of bond? (A) Covalent Bonds (B) Hydrogen Bonds (C) Dipole-dipole Interactions (D) Ionic Bonds
(A) Covalent Bonds The pathogen of this rare disease most likely targets and destroys phosphodiester linkages (covalent bonds), which hold the DNA structural backbone together.
In which type of DNA would you find an organism's most important genetic information? (A) Single copy (B) Slightly repetitive (10+ repeats) (C) Highly repetitive (100+ repeats) (D) Extremely repetitive (1,000+ repeats)
(A) Single copy An organism's most important genetic information is mainly found on the chromosome where there are high amounts of single copy DNA.
Watson and Crick built upon the work of many other scientists. Which of the following best describes Rosalind Franklin's contribution? (A) The Diffraction Patterns indicate Phosphates must be on the outside of some helical structure. (B) Nitrogenous bases must pair to their complement in DNA. (C) The amount of A equals the amount of T, and the amount of C equals the amount of G. (D) None of the above.
(A) The Diffraction Patterns indicate Phosphates must be on the outside of some helical structure.
What can you infer concerning a cell that has a lot of telomerase compared to a cell that has very little? (A) The cell must replicate more often. (B) The cell must replicate less often. (C) The cell must produce less genetic mutations. (D) The cell must produce more genetic mutations.
(A) The cell must replicate more often. When a cell has greater amounts of telomerase, that cell probably replicates more frequently than other cells with less telomerase.
Which carbons of ribose are involved in the ribose ring formation? (A) C-1 and C-2 (B) C-1 and C-4 (C) C-2 and C-3 (D) C-2 and C-5
(B) C-1 and C-4 The lone pair on the oxygen attached 4th carbon (C-4) forms a bond with C-1 which then leads to the C-1 oxygen forming a bond with a hydrogen (forming a hydroxyl
What enzyme is responsible for adding nucleotides to the DNA template strands? (A) DNA Primase (B) DNA Polymerase (C) DNA Ligase (D) DNA Helicase
(B) DNA Polymerase DNA polymerase is the enzyme responsible for adding nucleotides to the DNA template strands.
In which of the following stages of the Cell Cycle would you expect Mismatch Repair to be active? (A) G1 (B) G2 (C) S (D) M
(B) G2 In the G2 phase (right after S phase, where transcription occurs) is where the Mismatch Repair Mechanism is active.
Which of the following statements about Base Pairing are true? I. The Adenine-Thymine and Cytosine-Guanine pairing is referred to as Watson-Crick base pairing II. There is also "Wobble Base Pairing", where two nucleotides that are not part of the Watson-Crick Base Pairing can pair. III. There are instances where DNA can undergo Wobble Base Pairing. (A) I only (B) I and II only (C) I and III only (D) I, II and III
(B) I and II only Each of the following statements are true: I. The Adenine-Thymine and Cytosine-Guanine pairing is referred to as Watson-Crick base pairing II. There is also "Wobble Base Pairing", where two nucleotides that are not part of the Watson-Crick Base Pairing can pair. III. There are instances where RNA can undergo Wobble Base Pairing.
Which part in the structure of DNA is acidic? I. Sugar II. Phosphate III. Nitrogenous Bases (A) I Only (B) II Only (C) II and III Only (D) I, II, and III
(B) II Only The phosphate group in DNA is acidic.
Which of the following types of DNA Polymerases (which are all found in Prokaryotes) can also be found in Eukaryotes? I. DNA Polymerase I II. DNA Polymerase II III. DNA Polymerase III (A) I only (B) II only (C) I and III only (D) I, II and III
(B) II only DNA Polymerase II is the only DNA Polymerase found in Eukaryotes! All three types are found in Prokaryotes.
CRB Which of the following is the proper term for any compound that can cause mutations? (A) Cancerous (B) Mutagen (C) Carcinogen (D) None of the above
(B) Mutagen A Mutagen is any compound that can cause mutation. This differs from a Carcinogen, which would aid in the process of tumor development in general.
Which of the following nitrogenous bases is NOT found in mRNA? (A) A (B) T (C) C (D) G
(B) T You will not find the base Thymine in RNA. Instead, Adenine will pair with Uracil (A-U). The base pair Cytosine-Guanine (C-G) remains the same.
RNA contains __________. DNA contains _____________. (A) ribose, ribose (B) ribose, deoxyribose (C) deoxyribose, deoxyribose (D) deoxyribose, ribose
(B) ribose, deoxyribose Ribose is found in RNA, while deoxyribose is found in DNA.
If you add three phosphate groups to ____________, you will get the "Powerhouse of the Cell" and high-energy molecule ____________. (A) Adenine, ATP (B) Guanine, GTP (C) Adenosine, ATP (C) Guanosine, GTP
(C) Adenosine, ATP If you add three phosphate groups to Adenosine, you will get the "Powerhouse of the Cell" and high-energy molecule ATP.
Fill in the blanks: The traditional DNA double helix is a right-handed helix that forms _____________; another competing form is _______________, which is known for its zig-zag appearance and being a left-handed helix. (A) A-DNA, B-DNA (B) A-DNA, Z-DNA (C) B-DNA, Z-DNA (D) B-DNA, A-DNA
(C) B-DNA, Z-DNA The traditional DNA double helix is a right-handed helix that forms B-DNA; another competing form is Z-DNA, which is known for its zig-zag appearance and being a left-handed helix.
What enzyme is responsible joining the Okazaki fragments together? (A) DNA Primase (B) DNA Polymerase (C) DNA Ligase (D) DNA Helicase
(C) DNA Ligase DNA ligase is responsible for joining the Okazaki fragments together.
DNA Polymerase I is an ____________________, and DNA Polymerase III is an ____________________. (A) Endonuclease, Endonuclease (B) Endonuclease, Exonuclease (C) Exonuclease, Exonuclease (D) Exonuclease, Endonuclease
(C) Exonuclease, Exonuclease DNA Polymerase I is an Exonuclease, and DNA Polymerase III is an Exonuclease.
What components is the backbone of DNA made up of? I. Sugar II. Phosphate III. Nitrogenous Bases (A) I Only (B) II Only (C) I and II Only (D) I, II, and III
(C) I and II Only The backbone of DNA is made up of a combination of sugar and phosphate.
Where in the chromosome would you most likely find repetitive DNA? I. Centromeres II. Telomeres III. Between the Centromeres and Telomeres (A) I Only (B) II Only (C) I and II Only (D) I, II, and III
(C) I and II Only You would most likely find repetitive DNA near the centromeres (center of chromosomes) and at the telomeres (ends of the chromosomes).
Place the steps of a polymerase chain reaction (PCR) in the correct order: I. Annealing II. Extension III. Denaturation (A) III > II > I (B) II > III > I (C) III > I > II (D) I > II > III
(C) III > I > II The polymerase chain reaction (PCR) happens subsequently in the following order: (1) Denaturation (2) Annealing (3) Extension
Put the following steps of the Mismatch Repair Mechanism in order: I. DNA Ligase repairs the DNA backbone. II. Exonuclease removes the misplaced nucleotide. III. DNA Polymerase adds the correct nucleotide. IV. The mismatched DNA is marked with a cut. (A) IV, I, II, III (B) I, IV, II, III (C) IV, II, III, I (D) I, II, III, IV
(C) IV, II, III, I Mismatch Repair Mechanism entails the following steps in order: 1. The mismatched DNA is marked with a cut. 2. Exonuclease removes the misplaced nucleotide (and perhaps some of its neighbors) from the newly synthesized strand. 3. DNA Polymerase adds the correct nucleotide. 4. DNA Ligase repairs the DNA backbone by binding the newly placed nucleotide to the neighboring nucleotides.
Since DNA Ligase does not have Proofreading capabilities, which of the following is most likely to have mutations? (A) Beginning of a strand (B) Leading Strand (C) Lagging Strand (D) End of a strand
(C) Lagging Strand Since DNA Ligase does not have Proofreading capabilities, the lagging strand is most likely to have mutations.
What would happen during replication if there were no telomeres on the chromosome? (A) Replication would produce mutations. (B) Replication would continue on forever. (C) Replication would cause the loss of genetic material. (D) Replication would co-occur with Transcription.
(C) Replication would cause the loss of genetic material. If there were no telomeres on the chromosome, then important genetic information would go un-replicated at the ends of the chromosomes, resulting in the loss of genetic material.
After replication is completed, there is a thymine base-paired with a guanine. What will fix this issue? (A) The DNA Polymerase III Proofreading Mechanism (B) The Base Excision Repair Mechanism (C) The Mismatch Repair Mechanism (D) The Nucleotide Excision Repair Mechanism
(C) The Mismatch Repair Mechanism The mismatch repair mechanism happens after DNA replication. Through this mechanism, mismatches in the DNA sequence missed by the DNA polymerases during replication will be fixed.
Watson and Crick built upon the work of many other scientists. Which of the following best describes Chargaff's Rules? (A) The Diffraction Patterns indicate Phosphates must be on the outside of some helical structure. (B) Nitrogenous bases must pair to their complement in DNA. (C) The amount of A equals the amount of T, and the amount of C equals the amount of G. (D) None of the above.
(C) The amount of A equals the amount of T, and the amount of C equals the amount of G.
You look into a microscope and see a pyrimidine dimer in DNA. What has the DNA likely been exposed to? (A) X-rays (B) Visible Light (C) Infrared Light (D) Ultraviolet Light
(D) Ultraviolet Light You can conclude that the DNA has been exposed to UV rays because UV rays cause the formation of pyrimidine dimers.
DNA replication is: (A) Fast and precise (B) Fast but not precise (C) Slow and precise (D) Slow but not precise
A) Fast and precise DNA replication is very fast and very precise. For example, DNA polymerase can add an average of 700 base pairs per second and makes only 1 mistake every 10 million nucleotides.
Which of the five nitrogenous bases are purines?
Adenine and guanine are both purines. Both have 2 rings.
What is the difference between the two most common electrophoresis types: agarose (polyacrylamide gel electrophoresis) vs. sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis?
Agarose gel (polyacrylamide gel electrophoresis) is used for larger DNA fragments and the mobility of DNA fragments in this gel depends on both size and charge. Sodium dodecyl sulfate (SDS)-polyacrylamide gel is used for smaller macromolecules (either small DNA or small proteins) and the mobility through this gel strictly depends on size alone since SDS disrupts all noncovalent interactions. Also, SDS will cause the protein to unfold.
What is the role of an antioxidant molecule in preventing DNA damage/mutation?
An antioxidant molecule helps protect DNA aganist the damaging effect of reactive oxygen species.
Which enzyme is involved in a nucleotide excision repair? An endonuclease or exonuclease?
An endonuclease is involved in a nucleotide excision repair because nucleotides need to be removed from the middle of a DNA strand.
What is the complementary DNA strand for 3'-GATTACA-5'? (A) 5'-CUAAUGU-3' (B) 5'-GATTACA-3' (C) 5'-CTAATGT-3' (D) 5'-GAUUACA-3'
C) 5'-CTAATGT-3' 5'-CTAATGT-3' 3'-GATTACA-5' The base pairs are A-T and C-G when synthesizing DNA. The strands are antiparallel, with the 3' end of one strand complementing the 5' end of the other strand.
What enzyme is responsible for adding RNA primers? (a) DNA Primase (b) RNA Polymerase (c) RNA Ligase (d) DNA Helicase
DNA primase is the enzyme is responsible for adding RNA primers, which will allow DNA Polymerase to bind to the DNA and start adding nucleotides in the 5'-3' direction.
True or false? Tumor Suppression genes are often described as being a "Two-Hit Model", since the two alleles must be mutated in the same tissue.
False. Tumor Suppression genes are often described as being a "Two-Hit Model", since the two alleles must be mutated in the same Cell.
What is the primary responsibility of Helicase in terms of DNA replication?
Helicase is the enzyme is responsible for breaking the hydrogen bonds between the nitrogenous bases (unwinding the helix).
Compare Heterochromatin and Euchromatin, focusing on the role of Histones.
Heterochromatin is tightly packed around histones, preventing transcription. Euchromatin is transcriptionally active and not tightly packed around Histones, and is often seen during Interphase.
Describe what would happen if two purines or two pyrimidines were mistakenly paired together in DNA in a stable way.
If two purines are paired together, then there will be four rings between the nitrogenous bases, messing up the spacing of the double helix. If two pyrimidines were paired together, there will be only two rings between the nitrogenous bases, also affecting the spacing of the helix.
CRB Compare Missense, Nonsense and Frameshift Mutations.
Missesne mutations replace one amino acid for another. Nonsense mutations will add a premature stop codon, and can also be called a Truncation Mutation. Frameshift mutations alter the number of nucleotides in the sequence, and will affect the amino acid sequence for all following codons.
There are only three steps to Nucleotide Excision Repair. What are they?
Nucleotide Excision Repair entails the following three steps: (1) Endonuclease removes pyramidine dimer and surrounding nucleotides. (2) DNA Polymerase will fill in the gap with the proper nucleotides. (3) DNA Ligase will repair the backbone by connecting the new nucleotides to the old nucleotides.
What are Okazaki fragments?
Okazaki fragments are newly synthesized DNA fragments that are formed on the lagging template strand during DNA replication. Remember that DNA polymerase can only add nucleotides in the 5' to 3' direction, so DNA can only be added to the lagging strand as more of the lagging strand is exposed.
What is the primary structural difference between purines and pyrimidines?
Purines contain two rings in their structure, while pyrimidines contain only one ring in their structure.
Superoxide anions (O2) and peroxides are examples of what kind of DNA damage? Exogeneous or endogeneous agents?
Superoxide anions and peroxides are examples of Reactive Oxygen Species (ROS), which are endogenous agents that can cause DNA damage.
What about the lagging strand makes the process of DNA replication a bit more complicated?
The lagging strand is "unzipped" in the direction of 3' to 5', but DNA polymerase does not add nucleotides in the 3' to 5' direction. Okazaki fragments must be made to accommodate this opposing direction and joined together by DNA ligase.
Between the leading strand and lagging strand, which is more prone to mutations? Why?
The lagging strand is more prone to mutations because it must constantly start and stop the process of DNA replication and contains many more RNA primers, all of which must be removed and filled in with DNA.
Which strand of DNA is replicated more slowly during DNA replication? The Leading or the Lagging Strand?
The lagging strand of DNA is replicated more slowly during DNA replication because the process requires more work. In order for the DNA polymerase to add in the 5' to 3' direction, RNA primers and Okazaki fragments must be created over and over again. This also requires replacing the RNA primers with DNA and binding the Okazaki fragments together using DNA Ligase over and over again.
How does the mismatch repair mechanism distinguish between the parent strand and the newly synthesized strand that has the mistake on it in bacteria?
The mismatch repair mechanism can distinguish between the parent strand and the newly synthesized strand that has the mistake on it because the parent strand will have more methylation
What is the purpose of Polymerase Chain Reaction (PCR)?
The purpose of PCR is to generate tons and tons of copies of a single fragment of DNA that you are interested in. This is essential for researchers since it would be very hard to work with just a single copy of DNA since they are so tiny and fragile. Having many copies allows you to better test and visualize the DNA you are interested in.
True or false? These levels of methylation can also impact the transcriptional activity of the DNA.
True. These levels of methylation can also impact the transcriptional activity of the DNA.
True or false? To further compact the DNA in sperm, the majority of Histones are replaced with Protamines.
True. To further compact the DNA in sperm, the majority of Histones are replaced with Protamines.
On which side of the gel electrophoresis (negative electrode or positive electrode) would you place samples of DNA fragment?
You would place samples of DNA fragments on the same side of the gel as the negative electrode. This way, DNA (with its negatively-charged phosphate backbone) will migrate across the gel towards the positive electrode.
