Lesson 4: DNA

Describe how the name "Deoxyribonucleic Acid" relates to the structure of DNA.

"Deoxyribose" refers to the sugar monomer, "nucleic" refers to the fact that DNA is found in the nucleus, and "Acid" refers to the acidic phosphate group.

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!"

*CRB* 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.

*CRB* 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 the 3' to 5' 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 Single copy DNA also has low mutation rates

*CRB* 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 kicking off one of the bonds of the carbonyl, which then leads to the C-1 oxygen forming a bond with a hydrogen (forming a hydroxyl group).

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.

*CRB* 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.

*CRB* 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.

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.

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.

*CRB* 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 (D) 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.

*CRB* 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.

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 where chromatids are attached) and at the telomeres (ends of the chromosomes). Repetitive DNA has a higher mutation rate than single copy. many repetitive DNA contain genes that are transcribed or translated

Which of the following are classes of nitrogenous bases? I. Purines II. Pyridines III. Pyrimidines (A) I and II Only (B) II and III Only (C) I and III Only (D) I, II, and III

(C) I and III Only The two classes of nitrogenous bases are Purines and Pyrimidines.

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.

*CRB* 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.

*CRB* Which of the following statements about Transposons are FALSE? (A) Transposons all code for Transposase proteins that can catalyze the movement of Transposon sequences in the genome. (B) Transposases come in three different structures. (C) Transposases are found only in Eukaryotes. (D) Transposases in Eukaryotes are thought to be degenerate retroviruses.

(C) Transposases are found only in Eukaryotes. Transposases are found in both Prokaryotes and Eukaryotes.

How many chromosomes are in one human cell? (A) 22 (B) 23 (C) 44 (D) 46

(D) 46 In humans, each cell normally contains 23 pairs of chromosomes, for a total of 46 chromosomes.

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.

Where would you find the highest rate of mutation in DNA? (A) Single copy (B) Slightly repetitive (10+ repeats) (C) Highly repetitive (100+ repeats) (D) Extremely repetitive (1,000+ repeats)

(D) Extremely repetitive (1,000+ repeats) You would find a higher rate of mutation in repetitive DNA because they do not contain genes and are not transcribed nor translated.

*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.

Each DNA monomer (nucleotide) is made up of which of the following components? I. Sugar II. Phosphate III. Nitrogenous Bases (A) I Only (B) II Only (C) I and II Only (D) I, II, and III

(D) I, II, and III Each DNA molecule is composed of a five-carbon sugar, a nitrogenous base, and one or more phosphate groups.

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 act as a buffer zone not containing any important genes fro replication and it allows telomerase to finish the replication all the way up to right before the telomere where he important gene ends 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. Recall that at the end of replication, the NRA primer has to be removed and there will be 5' over hang that telomeres have to come fix

*CRB* Watson and Crick built upon the work of many other scientists. Which of the following best describes Linus Pauling'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.

(D) None of the above. Linus Pauling is actually known for proposing a triple helical DNA model!

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.

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 (replication phase) 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).

The phosphodiester linkage forms between:

A free 5' phosphate and a free 3' OH

Which of the five nitrogenous bases are purines?

Adenine and guanine are both purines. Both have 2 rings.

Function of RNA?

After transcription, RNA can assist in protein synthesis by undergoing translation

Why is DNA able to run antiparallel to each other?

Because bases on each side of DNA are complementary to each each other

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.

*CRB* 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.

What is the difference in RNA and DNA structure?

DNA exists in a double helix where as RNA exist predominantly as a single strand due to having a different sugar

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.

*CRB* 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.

*CRB* True or false? To go from Adenosine to Adenine, you add the five-carbon sugar.

False. To go from Adenosine to Adenine, you REMOVE the five-carbon sugar.

How do you number the five-carbon sugar pentose found in DNA?

Give the carbon that is bound to two oxygens the lowest priority (C-1). Then start counting carbons around the ring until you get to the carbon that is outside the ring (C-5). This numbering system also works for the ribose in RNA.

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).

*CRB* 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.

*CRB* 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!

*CRB* 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.

What is the significance of the negative phosphate groups on the backbone of DNA?

It makes it hydrophilic so that DNA can interact with polar water molecules to stabilize the structure of DNA It also makes DNA more resistant to hydrolysis via a nucleophile. Note that typically when we have ester bonds, it can undergo hydrolysis where a nucleophile goes and breaks that bond but since we have negative charges on the phospahte group, it will repel the negative charge of the nucleophile.

What is the significance of the absence of the hydroxyl group on the 2' carbon of deoxyribose ?

It stabilizes the DNA structure by making it much more resistant to hydrolysis by different kinds of nucleophiles

What is the difference between a nucleoside or nucleotide?

Nucleoside is sugar group and a base. Nucleotide is a nucleoside added to one or more phosphates.

*CRB* 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.

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.

What is the difference between single copy DNA and repetitive DNA?

Single copy DNA is basically DNA sequence that does not repeat itself, such as -ATCCG-, while a repetitive DNA is a sequence that repeats itself, such as -ATCCGATCCGATCCG-. Single copy DNA tends to contain more genes than repetitive DNA.

Function of DNA?

Store genetic info in the nitrogenous bases and keep it accessible for cell so that it can be used to build a protein. It also passes down genetic info to offspring

What is the Meslson and Stahl experiment?

The Meselson-Stahl experiment is an experiment by Matthew Meselson and Franklin Stahl in 1958 which supported Watson and Crick's hypothesis that DNA replication was semiconservative.

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 does the enzyme telomerase do?

The enzyme telomerase lengthens the telomeres and brings them back to their original length.

Describe why the hydrogen bonds form?

The groups that the hydrogen is attached to pulls electron density away making hydrogen very positive... and then the groups Hydrogen attaches to are very negative.

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.

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 dispersive DNA replication?

The theory of dispersive DNA replication describes DNA replication that results in two pairs of double-helix DNA and each of the 4 DNA strands contains some old DNA and new DNA.

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.

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? 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.

*CRB* 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.

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).

What are the nucleosides found in RNA molecules?

adensosine guanosine cytidine uridine

The bond between the sugar group and the base is always between:

carbon 1 and nitrogen # q 1 on the purine or pyrimidine

What are the nucleosides found in DNA molecules?

deoxyadenosine deoxyguanosine deoxycitidine thymididine

DNA replication Step by step:

insert pics in anki

The 5' end of DNA has a free_____________ The 3' end of DNA has a free_____________

phosphate group hydroxyl group

What bonds hold nucleotides together to make nucleic acids?

phosphodiester bonds